Support for a new dynamic visualization.

draeger-lab · Aug 15, 2019 · 9c7d465 · 9c7d465
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diff --git a/examples/org/sbml/simulator/fba/CSVDataConverterTest.java b/examples/org/sbml/simulator/fba/CSVDataConverterTest.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  ContraintsUtilsTest.java 18:43:52 Meike Aichele$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -25,7 +23,6 @@
 
 /**
  * @author Meike Aichele
- * @version $Rev$
  * @date 13.06.2012
  * @since 1.0
  */

diff --git a/examples/org/sbml/simulator/fba/ConstraintsTest.java b/examples/org/sbml/simulator/fba/ConstraintsTest.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  ConstraintsTest.java 19:03:59 Meike Aichele$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -27,7 +25,6 @@
 
 /**
  * @author Meike Aichele
- * @version $Rev$
  * @date 13.06.2012
  * @since 1.0
  */

diff --git a/examples/org/sbml/simulator/fba/FluxBalanceAnalysisTest.java b/examples/org/sbml/simulator/fba/FluxBalanceAnalysisTest.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  FluxBalanceAnalysisTest.java 19:04:44 Meike Aichele$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -39,7 +37,6 @@
 
 /**
  * @author Meike Aichele
- * @version $Rev$
  * @date 17.06.2012
  * @since 1.0
  */

diff --git a/examples/org/sbml/simulator/fba/FluxMinimizationTest.java b/examples/org/sbml/simulator/fba/FluxMinimizationTest.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  FluxMinimizationTest.java 12:30:10 Meike Aichele$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -29,7 +27,6 @@
 
 /**
  * @author Meike Aichele
- * @version $Rev$
  * @date 09.06.2012
  * @since 1.0
  */

diff --git a/examples/org/sbml/simulator/fba/FluxMinimizationUtilsTest.java b/examples/org/sbml/simulator/fba/FluxMinimizationUtilsTest.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  FluxMinimizationUtilsTest.java 17:35:33 Meike Aichele$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -27,7 +25,6 @@
 
 /**
  * @author Meike Aichele
- * @version $Rev$
  * @date 13.06.2012
  * @since 1.0
  */

diff --git a/examples/org/sbml/simulator/fba/dynamic/DynamicFBAFluxMinIITest.java b/examples/org/sbml/simulator/fba/dynamic/DynamicFBAFluxMinIITest.java
@@ -1,6 +1,4 @@
 /*
- * $$Id${file_name} ${time} ${user}$$
- * $$URL${file_name} $$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -35,8 +33,9 @@
 import de.zbit.io.csv.CSVWriter;
 
 /**
- * @author Stephanie Tscherneck, Robin F&auml;hnrich, Roland Keller
- * @version $Rev$
+ * @author Stephanie Tscherneck
+ * @author Robin F&auml;hnrich
+ * @author Roland Keller
  * @since 1.0
  * ${tags}
  */

diff --git a/examples/org/sbml/simulator/fba/dynamic/DynamicFBATest.java b/examples/org/sbml/simulator/fba/dynamic/DynamicFBATest.java
@@ -1,10 +1,6 @@
 /*
- * $Id$URL:
- * https://rarepos.cs.uni-tuebingen
- * .de/svn-path/SBMLsimulator/trunk/examples/org/
- * sbml/simulator/fba/dynamic/DynamicFBATest.java $
- * --------------------------------------------------------------------- This
- * file is part of SBMLsimulator, a Java-based simulator for models of
+ * --------------------------------------------------------------------- 
+ * This file is part of SBMLsimulator, a Java-based simulator for models of
  * biochemical processes encoded in the modeling language SBML.
  * 
  * Copyright (C) 2007-2016 by the University of Tuebingen, Germany.
@@ -33,7 +29,6 @@
  * Test a dynamic flux balance analysis.
  * 
  * @author Robin F&auml;hnrich
- * @version $Rev$
  * @since 1.0
  */
 public class DynamicFBATest {

diff --git a/resources/org/sbml/simulator/gui/graph/DynamicGraph.xml b/resources/org/sbml/simulator/gui/graph/DynamicGraph.xml
@@ -21,10 +21,14 @@
   <entry key="TO_VIDEO_TOOLTIP">Save the dynamic visualization as a video. Resolution can be adjusted with resolution multiplier in options and the resulting speed of the video itself will be approximately the same as the chosen simulation speed.</entry>
   <entry key="GRAPHSHOT">Image</entry>
   <entry key="GRAPHSHOT_TOOLTIP">Take a screenshot of the whole graph. Resolution can be adjusted with resolution multiplier in options.</entry>  
+  <entry key="CONCENTRATIONGRAPH">Graph of metabolic concentration</entry>
+  <entry key="CONCENTRATIONGRAPH_TOOLTIP">Shows a graph with all metabolic concentrations over time and the current one.</entry>
   <entry key="NODELABELS">Nodelabels</entry>
   <entry key="NODELABELS_TOOLTIP">Switch for node labels.</entry>
   <entry key="REACTIONLABELS">Reactionlabels</entry>
   <entry key="REACTIONLABELS_TOOLTIP">Switch for reaction labels.</entry>
+  <entry key="CYCLE_SIMULATION">Loopsimulation</entry>
+  <entry key="CYCLE_SIMULATION_TOOLTIP">Simulation restarts over and over again</entry>
   <entry key="FAST">Fast</entry>
   <entry key="NORMAL">Normal</entry>
   <entry key="SLOW">Slow</entry>
@@ -36,12 +40,19 @@
   <entry key="NODECOLOR">Node color</entry>
   <entry key="NODESIZE_AND_COLOR">Abs.size/rel.color</entry>
   <entry key="NODECOLOR_AND_SIZE">Rel.size/abs.color</entry>
+  <entry key="FILL_LEVEL">Rel.Filling level/abs.color</entry>
   <entry key="GROUP_VISUALIZATION">Visualization</entry> 
   <entry key="VISUALIZATION_TOOLTIP">Chose visualization style and data for the dynamic visualization.</entry>
   <entry key="SEARCHBAR_TOOLTIP">Choose time point of visualization.</entry>
   <entry key="GENERATE_VIDEO">Generate video with {0}x{1} pixel.</entry>
   <entry key="SCREENSHOT_DONE">Picture sucessfully saved.</entry>
 
+  <!--  ConcentrationGraphUI  -->
+
+  <entry key="CONCENTRATION_GRAPH_TITLE">Concentration</entry>
+  <entry key="X_AXIS">Time</entry>
+  <entry key="Y_AXIS">Concentration</entry>
+
   <!-- DynamicController -->
 
   <entry key="VIDEO_FILEFILTER">Videofiles (*.mov, *.avi, *.mp4, *.mpg, *.wmv, *.flv)</entry>
@@ -79,6 +90,8 @@
   <entry key="USE_UNIFORM_NODE_COLOR_TOOLTIP">Enable/Disable uniform node colors instead of node colors given in legend.</entry>
   <entry key="UNIFORM_NODE_COLOR">Color for uniform node color</entry>
   <entry key="UNIFORM_NODE_COLOR_TOOLTIP">Sets the color for uniform node color.</entry>
+  <entry key="CHOOSE_OWN_NODE_COLORS">Choose concentration colors</entry>
+  <entry key="CHOOSE_OWN_NODE_COLORS_TOOLTIP">Choose colors of the concentrations on your own</entry>
   <entry key="GROUP_NODESIZE">Dynamic change of node size</entry>
   <entry key="GROUP_NODESIZE_TOOLTIP">Options for the dynamic change of node size.</entry>
   <entry key="GROUP_NODECOLOR">Dynamic change of node color</entry>
@@ -132,5 +145,16 @@
   <entry key="VIDEO_FORCE_RESOLUTION_MULTIPLIER_TOOLTIP">By enabling this option you can force to use the resolution multiplier even if the video output resolution would be big enough.</entry>
   <entry key="VIDEO_DISPLAY_WINDOW">Picture whole graph</entry>
   <entry key="VIDEO_DISPLAY_WINDOW_TOOLTIP">Choose if the whole graph should be pictured in videos and screenshots or just the current display window.</entry>
+  <entry key="CAMERA_WAY_FILE">Camera animation</entry>
+  <entry key="CAMERA_WAY_FILE_TOOLTIP">Add file for camera animation</entry>
+  <entry key="SHOW_CAMERA_ANIMATION">Camera animation</entry>
+  <entry key="SHOW_CAMERA_ANIMATION_TOOLTIP">Shows the added camera animation in chosen speed, if play or video is pressed</entry>
+  <entry key="NO_CAMERA_ANIMATION">Without</entry>
+  <entry key="NO_CAMERA_ANIMATION_TOOLTIP">No camera animation is shown</entry>
+
+  <!-- Rearrange the cycles nicely -->
+  <entry key="FILE_WITH_REACTIONNODES">File with reactionglyphs</entry>
+  <entry key="FILE_WITH_SPECIES">File with speciesglyphs</entry>
+  <entry key="RADIUS_OF_CIRCLE">Radius of circle</entry>
 
 </properties>
diff --git a/resources/org/sbml/simulator/gui/graph/DynamicGraph_de.xml b/resources/org/sbml/simulator/gui/graph/DynamicGraph_de.xml
@@ -21,10 +21,14 @@
   <entry key="TO_VIDEO_TOOLTIP">Speichert die dynamische Visualisierung als Video. Die Auflösung kann über den Auflösungsmultiplikator in den Optionen angepasst werden und die Videogeschwindigkeit ist annähernd dieselbe, wie die eingestellte Simulationsgeschwindigkeit.</entry>
   <entry key="GRAPHSHOT">Bild</entry>
   <entry key="GRAPHSHOT_TOOLTIP">Speichert das aktuelle Netzwerk als Bilddatei. Die Auflösung kann über den Auflösungsmultiplikator in den Optionen angepasst werden.</entry>   
+  <entry key="CONCENTRATIONGRAPH">Graph der metabolischen Konzentrationen</entry>
+  <entry key="CONCENTRATIONGRAPH_TOOLTIP">Zeigt einen Graph mit allen metabolischen Konzentrationen insgesamt und zum aktuellen Zeitpunkt</entry>
   <entry key="NODELABELS">Knotenbeschriftung</entry>
   <entry key="NODELABELS_TOOLTIP">Blendet die Konzentrationen ein/aus.</entry>
   <entry key="REACTIONLABELS">Reaktionenbeschriftung</entry>
   <entry key="REACTIONLABELS_TOOLTIP">Blendet die Reaktionsgeschwindigkeiten ein/aus.</entry>
+  <entry key="CYCLE_SIMULATION">Loopsimulation</entry>
+  <entry key="CYCLE_SIMULATION_TOOLTIP">Simulation wird immer wieder von vorne gestartet</entry>
   <entry key="FAST">Schnell</entry>
   <entry key="NORMAL">Normal</entry>
   <entry key="SLOW">Langsam</entry>
@@ -36,12 +40,19 @@
   <entry key="NODECOLOR">Knotenfarbe</entry>
   <entry key="NODESIZE_AND_COLOR">Abs.Größe/rel.Farbe</entry>
   <entry key="NODECOLOR_AND_SIZE">Rel.Größe/abs.Farbe</entry>
+  <entry key="FILL_LEVEL">Rel.Füllstände/abs.Farbe</entry>
   <entry key="GROUP_VISUALIZATION">Visualisierung</entry>
   <entry key="VISUALIZATION_TOOLTIP">Wählen Sie die Art der dynamischen Visualisierung und die zu visualisierenden Daten aus.</entry>
   <entry key="SEARCHBAR_TOOLTIP">Stellen Sie den Zeitpunkt der Visualisierung ein.</entry>
   <entry key="GENERATE_VIDEO">Erzeuge Video mit {0}x{1} Pixel.</entry>
   <entry key="SCREENSHOT_DONE">Bild erfolgreich gespeichert.</entry>
 
+  <!--  ConcentrationGraphUI  -->
+
+  <entry key="CONCENTRATION_GRAPH_TITLE">Konzentrationsübersicht</entry>
+  <entry key="X_AXIS">Zeit</entry>
+  <entry key="Y_AXIS">Konzentrationen</entry>
+
   <!-- DynamicController -->
 
   <entry key="VIDEO_FILEFILTER">Videodateien (*.mov, *.avi, *.mp4, *.mpg, *.wmv, *.flv)</entry>
@@ -77,6 +88,8 @@
   <entry key="MAX_NODE_SIZE_TOOLTIP">Bei dynamischer Änderung der Knotengröße, definiert dies die maximale Knotengröße.</entry>
   <entry key="USE_UNIFORM_NODE_COLOR">Einheitliche Knotenfarbe</entry>
   <entry key="USE_UNIFORM_NODE_COLOR_TOOLTIP">Einheitliche Knotenfarbe, anstatt den Farben in der Legende.</entry>
+  <entry key="CHOOSE_OWN_NODE_COLORS">Konzentrationsfarben selbst wählen</entry>
+  <entry key="CHOOSE_OWN_NODE_COLORS_TOOLTIP">Alle Farben für die Konzentrationen selbst wählen</entry>
   <entry key="UNIFORM_NODE_COLOR">Knotenfarbe</entry>
   <entry key="UNIFORM_NODE_COLOR_TOOLTIP">Farbeinstellung für die einheitliche Knotenfarbe.</entry>
   <entry key="GROUP_NODESIZE">Dynamische Änderung der Knotengröße</entry>
@@ -132,5 +145,17 @@
   <entry key="VIDEO_FORCE_RESOLUTION_MULTIPLIER_TOOLTIP">Mit dieser Option kann der Auflösungsmultiplikator erzwungen werden auch wenn die Videoauflösung groß genug wäre.</entry>
   <entry key="VIDEO_DISPLAY_WINDOW">Komplettes Netzwerk abbilden</entry>
   <entry key="VIDEO_DISPLAY_WINDOW_TOOLTIP">Wählen Sie, ob das komplette Netzwerk auf Bildern und Videos dargestellt werden soll oder nur die aktuelle Ansicht.</entry>
+  <entry key="CAMERA_WAY_FILE">Kameraanimation</entry>
+  <entry key="CAMERA_WAY_FILE_TOOLTIP">Füge Datei für Kameraanimation hinzu</entry>
+  <entry key="SHOW_CAMERA_ANIMATION">Kameraanimation</entry>
+  <entry key="SHOW_CAMERA_ANIMATION_TOOLTIP">Zeigt die geladene Kameraanimation bei Simulationsstart in gewählter Geschwindigkeit</entry>
+  <entry key="NO_CAMERA_ANIMATION">Ohne</entry>
+  <entry key="NO_CAMERA_ANIMATION_TOOLTIP">Es wird keine Kameraanimation gezeigt</entry>
+
+  <!-- Rearrange the cycles nicely -->
+
+  <entry key="FILE_WITH_REACTIONNODES">Datei mit Reaktionsknoten</entry>
+  <entry key="FILE_WITH_SPECIES">Datei mit Metaboliten</entry>
+  <entry key="RADIUS_OF_CIRCLE">Radius des Kreises</entry>
 
 </properties>
diff --git a/resources/org/sbml/simulator/gui/graph/GPL_CONCENTRATION.png b/resources/org/sbml/simulator/gui/graph/GPL_CONCENTRATION.png
diff --git a/resources/org/sbml/simulator/gui/html/package-info.java b/resources/org/sbml/simulator/gui/html/package-info.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -20,7 +18,6 @@
  * Longer user messages that are displayed by the graphical user interface can
  * be found in this package. These are stored as web pages in HTML format.
  * 
- * @version $Rev$
  * @since 1.0
  */
 package org.sbml.simulator.gui.html;
diff --git a/resources/org/sbml/simulator/gui/img/package-info.java b/resources/org/sbml/simulator/gui/img/package-info.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -20,7 +18,6 @@
  * All icons that are used by the graphical user interface are collected in this
  * package.
  * 
- * @version $Rev$
  * @since 1.0
  */
 package org.sbml.simulator.gui.img;
diff --git a/resources/org/sbml/simulator/locales/package-info.java b/resources/org/sbml/simulator/locales/package-info.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -21,7 +19,6 @@
  * used by the graphical or the command line user interface are all gathered
  * in this package.
  * 
- * @version $Rev$
  * @since 1.0
  */
 package org.sbml.simulator.locales;
diff --git a/src/org/sbml/optimization/EstimationInitOperator.java b/src/org/sbml/optimization/EstimationInitOperator.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models of biochemical processes encoded in the modeling language SBML.
  *
@@ -37,7 +35,6 @@
  * well as multiple publications about evolutionary algorithms.
  * 
  * @author Roland Keller
- * @version $Rev$
  */
 public class EstimationInitOperator implements InterfaceInitialization {
 

diff --git a/src/org/sbml/optimization/EvA2GUIStarter.java b/src/org/sbml/optimization/EvA2GUIStarter.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -42,7 +40,6 @@
  * 
  * @author Marcel Kronfeld
  * @date 2010-09-01
- * @version $Rev$
  * @since 1.0
  */
 public class EvA2GUIStarter {

diff --git a/src/org/sbml/optimization/QuantityRange.java b/src/org/sbml/optimization/QuantityRange.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -46,7 +44,6 @@
  * @author Andreas Dr&auml;ger
  * @author Roland Keller
  * @date 2010-09-09
- * @version $Rev$
  * @since 1.0
  */
 public class QuantityRange implements Cloneable, Serializable {

diff --git a/src/org/sbml/optimization/package-info.java b/src/org/sbml/optimization/package-info.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -22,7 +20,6 @@
  * 
  * @author Marcel Kronfeld
  * @author Andreas Dr&auml;ger
- * @version $Rev$
  * @since 1.0
  */
 package org.sbml.optimization;
diff --git a/src/org/sbml/optimization/problem/EstimationOptions.java b/src/org/sbml/optimization/problem/EstimationOptions.java
@@ -1,6 +1,4 @@
 /*
- * $Id:  EstimationOptions.java 16:12:42 draeger$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of Simulation Core Library, a Java-based library for
  * of biochemical processes encoded in the modeling language SBML.
@@ -38,7 +36,6 @@
  * process.
  * 
  * @author Andreas Dr&auml;ger
- * @version $Rev$
  * @since 1.0
  * @date 2011-03-23
  */

diff --git a/src/org/sbml/optimization/problem/EstimationProblem.java b/src/org/sbml/optimization/problem/EstimationProblem.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -60,7 +58,6 @@
 /**
  * @author Andreas Dr&auml;ger
  * @date 2010-08-24
- * @version $Rev$
  * @since 1.0
  */
 public class EstimationProblem extends AbstractProblemDouble implements

diff --git a/src/org/sbml/optimization/problem/package-info.java b/src/org/sbml/optimization/problem/package-info.java
@@ -1,6 +1,4 @@
 /*
- * $Id$
- * $URL$
  * ---------------------------------------------------------------------
  * This file is part of SBMLsimulator, a Java-based simulator for models
  * of biochemical processes encoded in the modeling language SBML.
@@ -24,7 +22,6 @@
  * 
  * @author Andreas Dr&auml;ger
  * @author Marcel Kronfeld
- * @version $Rev$
  * @since 1.0
  */
 package org.sbml.optimization.problem;