From 5071a0aa2a07d1f514e8c2fd0b6b44a8705ae5db Mon Sep 17 00:00:00 2001 From: John May Date: Fri, 20 Jan 2017 16:20:54 +0000 Subject: [PATCH] Resolve unexpected

tag --- .../src/main/java/org/openscience/cdk/Element.java | 2 +- .../src/main/java/org/openscience/cdk/Isotope.java | 6 +++--- .../java/org/openscience/cdk/interfaces/IElement.java | 1 - .../cdk/isomorphism/matchers/QueryAtom.java | 11 +++++------ .../cdk/fingerprint/HybridizationFingerprinter.java | 4 ++-- .../cdk/graph/AtomContainerAtomPermutor.java | 4 ++-- 6 files changed, 13 insertions(+), 15 deletions(-) diff --git a/base/data/src/main/java/org/openscience/cdk/Element.java b/base/data/src/main/java/org/openscience/cdk/Element.java index b6eaabc313..f06a248637 100644 --- a/base/data/src/main/java/org/openscience/cdk/Element.java +++ b/base/data/src/main/java/org/openscience/cdk/Element.java @@ -115,12 +115,12 @@ public Element(String symbol, Integer atomicNumber) { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Elements can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Element element = new Element("C");
      *   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
      *   if.configure(element);
      *
- *

* * @return The atomic number of this element * diff --git a/base/data/src/main/java/org/openscience/cdk/Isotope.java b/base/data/src/main/java/org/openscience/cdk/Isotope.java index 3877e38e0b..8bcd53992a 100644 --- a/base/data/src/main/java/org/openscience/cdk/Isotope.java +++ b/base/data/src/main/java/org/openscience/cdk/Isotope.java @@ -178,12 +178,12 @@ public void setExactMass(Double exactMass) { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The NaturalAbundance value * @@ -199,12 +199,12 @@ public Double getNaturalAbundance() { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The ExactMass value * @@ -221,12 +221,12 @@ public Double getExactMass() { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The atomic mass of this element * diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java index 9fa75438f5..a90e47ee3d 100644 --- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java +++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java @@ -40,7 +40,6 @@ public interface IElement extends IChemObject { * IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder()); * if.configure(element); * - *

* * @return The atomic number of this element * diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java index 1fddbc9ef0..71a702cea5 100644 --- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java +++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java @@ -487,12 +487,12 @@ public void setExactMass(Double exactMass) { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The NaturalAbundance value * @@ -508,12 +508,12 @@ public Double getNaturalAbundance() { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The ExactMass value * @@ -530,12 +530,12 @@ public Double getExactMass() { *

Once instantiated all field not filled by passing parameters * to the constructor are null. Isotopes can be configured by using * the IsotopeFactory.configure() method: + *

* 
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      *
- *

* * @return The atomic mass of this element * @@ -562,15 +562,14 @@ public void setMassNumber(Integer massNumber) { /** * Returns the atomic number of this element. * - *

Once instantiated all field not filled by passing parameters + *

Once instantiated all field not filled by passing parameters * to the constructor are null. Elements can be configured by using - * the IsotopeFactory.configure() method: + * the IsotopeFactory.configure() method:

* 
      *   Element element = new Element("C");
      *   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
      *   if.configure(element);
      *
- *

* * @return The atomic number of this element * diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java index fde885a0e2..87f222a9d2 100644 --- a/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java +++ b/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java @@ -50,14 +50,14 @@ * exclude candidates for a substructure search in a database. They are also a * means for determining the similarity of chemical structures. * - *

A fingerprint is generated for an AtomContainer with this code:

+ * 
A fingerprint is generated for an AtomContainer with this code:
  *   Molecule molecule = new Molecule();
  *   IFingerprinter fingerprinter =
  *     new HybridizationFingerprinter();
  *   BitSet fingerprint = fingerprinter.getFingerprint(molecule);
  *   fingerprint.size(); // returns 1024 by default
  *   fingerprint.length(); // returns the highest set bit
- * 

+ *
* *

The FingerPrinter assumes that hydrogens are explicitly given! * Furthermore, if pseudo atoms or atoms with malformed symbols are present, diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java b/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java index 985b050955..456d41550b 100755 --- a/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java +++ b/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java @@ -28,9 +28,9 @@ /** * An atom container atom permutor that uses ranking and unranking to calculate - * the next permutation in the series.

+ * the next permutation in the series. * - *

Typical use:

+ * 
Typical use:
  * AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(container);
  * while (permutor.hasNext()) {
  *   IAtomContainer permutedContainer = permutor.next();