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josemduartejosemduarte
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Javadoc fix: errors in structure-gui module
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Lines changed: 13 additions & 25 deletions

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‎biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java‎

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*
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*/
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/**
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* <BODY>
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* <P>
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* Tools for loading and saving ontologies.
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* </P>
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* </BODY>
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*/
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package org.biojava.nbio.ontology.io;

‎biojava-ontology/src/main/java/package-info.java‎

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*
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*/
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/**
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* <BODY>
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* <P>
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* A general-purpose API for ontologies.
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* These are directed graphs consisting of <code>Term</code> obects. Each
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* <P>Some interfaces and implementations from this package are extended in
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* {@link org.biojavax.ontology biojavax} to better facilitate their persistence to
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* biosql.</P>
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* </BODY>
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*/

‎biojava-structure-gui/src/main/java/demo/AFPFromFasta.java‎

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/**
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* Demo displaying a structural alignment from a FASTA file using {@link FastaAFPChainConverter}.
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*
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* @author dmyerstu
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* @see {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
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* See {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
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* {@link FastaStructureParser}
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* @author dmyerstu
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*/
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public class AFPFromFasta {
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java‎

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/**
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*
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* @param alignment The alignment to plot
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* @param background [Optional]A matrix of 'background colors' over which to draw the alignment.
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*
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* Originally designed as a matrix of RMSD values between AFPs, so it is colorized
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* accordingly from red (0) to black (>10).

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java‎

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/**
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* Tracks Memory allocated & used, displayed in graph form.
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* Tracks Memory allocated and used, displayed in graph form.
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*/
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public class MemoryMonitor extends JPanel {
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java‎

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import org.biojava.nbio.structure.gui.util.StructurePairSelector;
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/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
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/**
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* A Panel that allows user to specify PDB and chain ID, as well as sub-ranges
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*
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* @author Andreas
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*

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java‎

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/**
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* Constructor using a MultipleAlignment.
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*
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* @param multAln
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* @param colors
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* @param msa
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* @param jm
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*/
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public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm) {
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this();

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java‎

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/**
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* Set the title of the AlignmentJmol window.
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* @param label
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* @param title
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*/
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public void setTitle(String title){
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frame.setTitle(title);

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java‎

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*
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*/
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/**
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* <BODY>
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* <P>
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* Some event classes for the protein structure GUIs.
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* Possible start classes are one level higher at
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* org.biojava.nbio.structure.gui.BiojavaJmol, and org.biojava.nbio.structure.gui.AlignmentGui.
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* </P>
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* </BODY>
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*/
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package org.biojava.nbio.structure.gui.events;

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java‎

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*
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*/
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/**
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* <BODY>
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* <P>
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* A few convenience classes to view protein structures with Jmol (if it is on the classpath),
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* to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
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* Possible start classes are BiojavaJmol, AlignmentGui.
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* Also MVC interface for structure-gui
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* </P>
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* </BODY>
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*/
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package org.biojava.nbio.structure.gui;

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