<td>Default is no colour.</td>
</tr>
<tr>
+ <td>defaultColourNuc</td>
+ <td>A colour scheme (from the list above) to apply to Nucleotide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
+ <td>defaultColourProt</td>
+ <td>A colour scheme (from the list above) to apply to Peptide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
<td>userDefinedColour</td>
<td><p><em>Example:</em><br>
D,E=red; K,R,H=0022FF; c=yellow</p></td>
<param name="windowWidth" value="800"/>
<param name="showAnnotation" value="true"/>
<param name="showSequenceLogo" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
->UNIPROT|Q7LCB3/249-274
----SLEHTLPVNRETLKRKVSGNRCASPV----------
->UNIPROT|Q9VSE9/175-200
----GSGTSGGNGGGGGGGTSGGNATNASA----------
>UNIPROT|Q9IBD5/371-408
EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI-
>UNIPROT|Q9YGV9/522-559
EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT-
>UNIPROT|Q90ZM7/97-134
EGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT-
->UNIPROT|Q91445/24-61
-EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMT-
>UNIPROT|Q90ZM8/198-236
QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK
Pfam dc206a
PHOSPHORYLATION (S) b974a5
PHOSPHORYLATION (Y) 7d3881
-Cath 93b1d2
+Cath 93b1d1
ASX-TURN-IR 4ccc6e
BETA-BULGE-LOOP-5 4066da
CATMAT-4 4dc465
ST-MOTIF ac25a1
STARTGROUP uniprot
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
-Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
-Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
</p>
<table>
<tr>
- <td><img src="annotationColumnSelectionWithSM.gif"></td>
- <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="AnnotationColumnSelectionWithSM.gif"></td>
+ <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
</tr>
</table>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
- <em>29/09/2015</em></strong>
+ <em>6/10/2015</em></strong>
</div>
</td>
<td>
- <div align="center"></div>
+ <em>General</em>
+ <ul>
+ <li>Updated Spanish translations of localized text for 2.9</li>
+ </ul>
+ <em>Application</em><ul>
+ <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+ <li>Signed OSX InstallAnywhere installer</li></ul>
+ <em>Applet</em>
+ <ul><li>Split frame example added to applet examples page</li>
+ </ul>
</td>
<td>
<div align="left">
+ <em>General</em>
<ul>
<li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
- <li>Split frame example added to applet examples page</li>
- <li>Applet with Jmol examples not loading correctly</li>
- <li>Incorrect warning on deleting selected columns</li>
- <li>Annotations incorrectly rendered after BioJS export and reimport</li>
- <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
- <li>Spanish translations of localized text - updates needed for 2.9</li>
- <li>Provide signed OSX InstallAnywhere installer</li>
+ <li>Broken images in filter column by annotation dialog documentation</li>
+ <li>Feature colours not parsed from features file</li>
+ <li>Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description</li>
+
</ul>
+ <em>Application</em><ul>
+ <li>Annotations corrupted after BioJS export and reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
+ <li>Incorrect warning about deleting all data when deleting selected columns</li>
+ <li>Patch to build system for shipping properly signed JNLP templates for webstart launch</li>
+ <li>EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing</li>
+ <li>Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly</li>
+ <li>Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug</li>
+ <li>Split cDNA/Protein view position and geometry not recovered from jalview project</li>
+ <li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
+ </ul>
+ <em>Applet</em><ul>
+ <li>Reorder sequences mirrored in cDNA/Protein split frame</li>
+ <li>Applet with Jmol examples not loading correctly</li>
+ </ul>
</div>
</td>
</tr>
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
/**
* This interface should be implemented by complex file parser with the ability
*
* @return
*/
- public ColourSchemeI getColourScheme();
+ public String getGlobalColourScheme();
/**
* Retrieves the Column selection/hidden column from a complex file parser
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- // TODO need to trigger a repaint of the complementary panel - how?
- // would prefer to handle in SplitFrame but it is not overriding key
- // listener chiz
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
}
}
if (applet != null)
{
- String colour = applet.getParameter("defaultColour");
-
+ String colour = al.isNucleotide() ? applet
+ .getParameter("defaultColourNuc") : applet
+ .getParameter("defaultColourProt");
+ if (colour == null)
+ {
+ colour = applet.getParameter("defaultColour");
+ }
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
af = new AlignFrame(al, hiddenSeqs, colSel,
alignFrame.viewport.applet, "Cut & Paste input - "
+ format, false);
af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
- af.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setFollowingComplementScroll(true);
+ complementPanel.setDontScrollComplement(true);
complementPanel.scrollToCentre(sr, verticalOffset);
}
}
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
* true, suppresses invoking the same method recursively.
*/
- private boolean followingComplementScroll;
+ private boolean dontScrollComplement;
/**
* Creates a new AlignmentPanel object.
x = 0;
}
+ /*
+ * each scroll adjustment triggers adjustmentValueChanged, which resets the
+ * 'do not scroll complement' flag; ensure it is the same for both
+ * operations
+ */
+ boolean flag = isDontScrollComplement();
hscroll.setValues(x, hextent, 0, width);
+ setDontScrollComplement(flag);
vscroll.setValues(y, vextent, 0, height);
}
* If there is one, scroll the (Protein/cDNA) complementary alignment to
* match, unless we are ourselves doing that.
*/
- if (isFollowingComplementScroll())
+ if (isDontScrollComplement())
{
- setFollowingComplementScroll(false);
+ setDontScrollComplement(false);
}
else
{
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
+ /*
+ * set scroll bar positions; first suppress this being 'followed' in any
+ * complementary split pane
+ */
+ setDontScrollComplement(true);
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
}
/**
- * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
*
* @param b
*/
- protected void setFollowingComplementScroll(boolean b)
+ protected void setDontScrollComplement(boolean b)
{
- this.followingComplementScroll = b;
+ this.dontScrollComplement = b;
}
- protected boolean isFollowingComplementScroll()
+ protected boolean isDontScrollComplement()
{
- return this.followingComplementScroll;
+ return this.dontScrollComplement;
}
}
command = "";
}
jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
jmb.setFinishedInit(true);
}
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
- af.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
import jalview.structure.StructureSelectionManager;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
boolean showjconsole = jalview.bin.Cache.getDefault(
"SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
+ if (Platform.isAMac())
+ {
+ desktop.setDoubleBuffered(false);
+ }
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setFrameIcon(null);
-
+ if (Platform.isAMac())
+ {
+ frame.setIconifiable(false);
+ frame.setFrameIcon(null);
+ // frame.setDesktopIcon(null);
+ frame.setDoubleBuffered(false);
+ }
if (frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount, yOffset
}
/**
- * Explode the views in the given frame into separate AlignFrame windows.
+ * Explode the views in the given SplitFrame into separate SplitFrame windows.
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
+ * remember the split pane divider location - this is set to match the
+ * 'exploding' frame.
*
* @param sf
*/
* AlignmentPanel objects, including their AlignmentViewports, so the
* cdna/protein relationships between the viewports is carried over to the
* new split frames.
+ *
+ * explodedGeometry holds the (x, y) position of the previously exploded
+ * SplitFrame, and the (width, height) of the AlignFrame component
*/
AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
AlignFrame newTopFrame = new AlignFrame(topPanel);
- newTopFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT));
+ newTopFrame.setSize(oldTopFrame.getSize());
newTopFrame.setVisible(true);
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newTopFrame.setSize(geometry.getSize());
+ }
+
AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
- newBottomFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT));
+ newBottomFrame.setSize(oldBottomFrame.getSize());
newBottomFrame.setVisible(true);
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newBottomFrame.setSize(geometry.getSize());
+ }
+
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
JInternalFrame splitFrame = new SplitFrame(newTopFrame,
newBottomFrame);
- // either panel may hold previous exploded frame geometry
- Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
- .getExplodedGeometry();
if (geometry != null)
{
- splitFrame.setBounds(geometry);
+ splitFrame.setLocation(geometry.getLocation());
}
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
*/
public void gatherViews(GSplitFrame source)
{
+ /*
+ * special handling of explodedGeometry for a view within a SplitFrame: - it
+ * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+ * height) of the AlignFrame component
+ */
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
- myTopFrame.viewport.setExplodedGeometry(source.getBounds());
- myBottomFrame.viewport.setExplodedGeometry(source.getBounds());
+ myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myBottomFrame.getWidth(), myBottomFrame
+ .getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- // both panels refer to the same split frame geometry
- Rectangle position = sf.getBounds();
- topPanel.av.setExplodedGeometry(position);
- bottomPanel.av.setExplodedGeometry(position);
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
+ topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf
+ .getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
view.setViewName(av.viewName);
view.setGatheredViews(av.isGatherViewsHere());
- Rectangle position = ap.av.getExplodedGeometry();
- if (position == null)
+ Rectangle size = ap.av.getExplodedGeometry();
+ Rectangle position = size;
+ if (size == null)
{
- position = ap.alignFrame.getBounds();
+ size = ap.alignFrame.getBounds();
+ if (av.getCodingComplement() != null)
+ {
+ position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+ .getBounds();
+ }
+ else
+ {
+ position = size;
+ }
}
view.setXpos(position.x);
view.setYpos(position.y);
- view.setWidth(position.width);
- view.setHeight(position.height);
+
+ view.setWidth(size.width);
+ view.setHeight(size.height);
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
int width = (int) dnaFrame.getBounds().getWidth();
int height = (int) (dnaFrame.getBounds().getHeight()
+ proteinFrame.getBounds().getHeight() + 50);
+
+ /*
+ * SplitFrame location is saved to both enclosed frames
+ */
+ splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
Desktop.addInternalFrame(splitFrame, title, width, height);
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* @see AlignmentPanel#adjustmentValueChanged
*/
- ap.setFollowingComplementScroll(true);
+ ap.setDontScrollComplement(true);
if (ap.scrollToPosition(results, false))
{
seqCanvas.revalidate();
import jalview.jbgui.GAlignFrame;
import jalview.jbgui.GSplitFrame;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Component;
import java.awt.event.KeyListener;
import java.beans.PropertyVetoException;
import java.util.Map.Entry;
+import java.util.Set;
import javax.swing.AbstractAction;
import javax.swing.InputMap;
import javax.swing.JComponent;
import javax.swing.JMenuItem;
import javax.swing.KeyStroke;
+import javax.swing.UIDefaults;
+import javax.swing.UIManager;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
((AlignFrame) getBottomFrame()).getViewport());
- int width = ((AlignFrame) getTopFrame()).getWidth();
- // about 50 pixels for the SplitFrame's title bar etc
+ /*
+ * estimate width and height of SplitFrame; this.getInsets() doesn't seem to
+ * give the full additional size (a few pixels short)
+ */
+ UIDefaults defaults = UIManager.getDefaults();
+ Set<Object> keySet = defaults.keySet();
+ for (Object key : keySet)
+ {
+ System.out.println(key.toString() + " = "
+ + UIManager.get(key).toString());
+ }
+ int widthFudge = Platform.isAMac() ? 28 : 28; // Windows tbc
+ int heightFudge = Platform.isAMac() ? 50 : 50; // tbc
+ int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
int height = ((AlignFrame) getTopFrame()).getHeight()
- + ((AlignFrame) getBottomFrame()).getHeight() + 50;
- // about 65 pixels for Desktop decorators on Windows
- height = Math.min(height, Desktop.instance.getHeight() - 65);
+ + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
+ + heightFudge;
+ height = fitHeightToDesktop(height);
setSize(width, height);
adjustLayout();
}
/**
+ * Reduce the height if too large to fit in the Desktop. Also adjust the
+ * divider location in proportion.
+ *
+ * @param height
+ * in pixels
+ * @return original or reduced height
+ */
+ public int fitHeightToDesktop(int height)
+ {
+ // allow about 65 pixels for Desktop decorators on Windows
+
+ int newHeight = Math.min(height, Desktop.instance.getHeight() - 65);
+ if (newHeight != height)
+ {
+ int oldDividerLocation = getDividerLocation();
+ setDividerLocation(oldDividerLocation * newHeight / height);
+ }
+ return newHeight;
+ }
+
+ /**
* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
* Order).
*/
/*
-
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Hashtable colours,
+ public boolean parse(AlignmentI align, Map colours,
boolean removeHTML)
{
return parse(align, colours, null, removeHTML, false);
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source)
- .getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
alignFrame.getViewport().setShowSequenceFeatures(
showSeqFeatures);
alignFrame.getViewport().setFeaturesDisplayed(fd);
- alignFrame.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
}
else
{
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
import java.io.IOException;
import java.io.StringReader;
public static final String FILE_DESC = "HTML";
- private ColourSchemeI colourScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.showSeqFeatures = jsonFile.isShowSeqFeatures();
- this.colourScheme = jsonFile.getColourScheme();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
this.columnSelection = jsonFile.getColumnSelection();
this.displayedFeatures = jsonFile.getDisplayedFeatures();
this.showSeqFeatures = showSeqFeatures;
}
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setColourScheme(String globalColourScheme)
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
public ColumnSelection getColumnSelection()
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
}
+ else
+ {
+ return;
+ }
}
AlignmentDimension aDimension = ap.getAlignmentDimension();
{
break;
}
+ if (data == null)
+ {
+ break;
+ }
}
if (data.indexOf("{\"") > -1)
import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
import jalview.json.binding.biojson.v1.AlignmentPojo;
import jalview.json.binding.biojson.v1.AnnotationPojo;
-import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
public class JSONFile extends AlignFile implements ComplexAlignFile
{
- private ColourSchemeI colourScheme;
-
private static String version = new BuildDetails().getVersion();
private String webstartUrl = "http://www.jalview.org/services/launchApp";
public static final String FILE_DESC = "JSON";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+ {
+ jsonAlignmentPojo.setGlobalColorScheme("None");
+ }
+ }
if (exportSettings.isExportFeatures())
{
if (jvSettingsJsonObj != null)
{
- String jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
- setColourScheme(getJalviewColorScheme(jsColourScheme));
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
}
+
+
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
}
- ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
- grpColourScheme, displayBoxes, displayText, colourText,
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
+ displayBoxes, displayText, colourText,
startRes, endRes);
+ seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+ seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
.toString(), annotations);
this.annotations.add(alignAnnot);
}
-
} catch (Exception e)
{
e.printStackTrace();
}
}
- public static ColourSchemeI getJalviewColorScheme(
- String bioJsColourSchemeName)
- {
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
- || cs.getJalviewName()
- .equalsIgnoreCase(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
- }
- }
- return jalviewColor;
- }
-
- public String getGlobalColorScheme()
- {
- return globalColorScheme;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
- {
- this.globalColorScheme = globalColorScheme;
- }
-
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setGlobalColorScheme(String globalColourScheme)
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
@Override
annotations.add(annot);
}
}
- globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
validateSelection();
}
});
+ tbl_summary.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelection();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ btn_back_ActionPerformed();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_ok.isEnabled())
+ {
+ btn_ok_ActionPerformed();
+ }
+ evt.consume();
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ tabbedPane.requestFocus();
+ }
+ else
+ {
+ btn_back.requestFocus();
+ }
+ evt.consume();
+ break;
+ default:
+ return;
+ }
+ }
+ });
btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
btn_back.setText(MessageManager.getString("action.back"));
btn_back_ActionPerformed();
}
});
+ btn_back.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_back_ActionPerformed();
+ }
+ }
+ });
btn_ok.setEnabled(false);
btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
btn_ok_ActionPerformed();
}
});
+ btn_ok.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_ok_ActionPerformed();
+ }
+ }
+ });
+
btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
btn_cancel_ActionPerformed();
}
});
+ btn_cancel.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_cancel_ActionPerformed();
+ }
+ }
+ });
scrl_searchResult.setPreferredSize(new Dimension(500, 300));
scrl_searchResult
public class GSplitFrame extends JInternalFrame
{
+ protected static final int DIVIDER_SIZE = 5;
+
private static final long serialVersionUID = 1L;
private GAlignFrame topFrame;
private JSplitPane splitPane;
+ /*
+ * proportional position of split divider; saving this allows it to be
+ * restored after hiding one half and resizing
+ */
+ private double dividerRatio;
+
/**
* Constructor
*
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, topFrame,
bottomFrame);
splitPane.setVisible(true);
- final double ratio = bottomFrame.getHeight() == 0 ? 0.5d : topFrame
- .getHeight()
- / (double) (topFrame.getHeight() + bottomFrame.getHeight());
- splitPane.setDividerLocation(ratio);
- splitPane.setResizeWeight(ratio);
- splitPane.setDividerSize(5);
+
+ /*
+ * set divider split at 50:50, or restore saved split if loading from
+ * project
+ */
+ int topFrameHeight = topFrame.getHeight();
+ splitPane.setDividerSize(DIVIDER_SIZE);
+ if (topFrameHeight == 0)
+ {
+ setRelativeDividerLocation(0.5d); // as a proportion
+ }
+ else
+ {
+ int dividerPosition = topFrameHeight + DIVIDER_SIZE / 2;
+ splitPane.setDividerLocation(dividerPosition); // absolute position
+ }
+ splitPane.setResizeWeight(0.5d);
add(splitPane);
}
}
/**
- * Make the complement of the specified split component visible or hidden,
- * adjusting the position of the split divide.
+ * Makes the complement of the specified split component visible or hidden,
+ * restoring or saving the position of the split divide.
*/
public void setComplementVisible(Object alignFrame, boolean show)
{
+ /*
+ * save divider ratio on hide, restore on show
+ */
+ if (show)
+ {
+ setRelativeDividerLocation(dividerRatio);
+ }
+ else
+ {
+ this.dividerRatio = splitPane.getDividerLocation()
+ / (double) (splitPane.getHeight() - splitPane
+ .getDividerSize());
+ }
+
if (alignFrame == this.topFrame)
{
this.bottomFrame.setVisible(show);
{
this.topFrame.setVisible(show);
}
- if (show)
- {
- // SplitPane needs nudging to restore 50-50 split
- // TODO save/restore other ratios
- splitPane.setDividerLocation(0.5d);
- }
+
validate();
}
+
+ /**
+ * Set the divider location as a proportion (0 <= r <= 1) of the height <br>
+ * Warning: this overloads setDividerLocation(int), and getDividerLocation()
+ * returns the int (pixel count) value
+ *
+ * @param r
+ */
+ public void setRelativeDividerLocation(double r)
+ {
+ this.dividerRatio = r;
+ splitPane.setDividerLocation(r);
+ }
+
+ /**
+ * Sets the divider location (in pixels from top)
+ *
+ * @return
+ */
+ protected void setDividerLocation(int p)
+ {
+ splitPane.setDividerLocation(p);
+ }
+
+ /**
+ * Returns the divider location (in pixels from top)
+ *
+ * @return
+ */
+ protected int getDividerLocation()
+ {
+ return splitPane.getDividerLocation();
+ }
}
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Arrays;
toolTipText = getValueAt(rowIndex, colIndex).toString();
} catch (Exception e)
{
- e.printStackTrace();
+ // e.printStackTrace();
}
toolTipText = (toolTipText == null ? null
: (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
{
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
+ tbl_summary.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ validateSelections();
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ validateSelections();
+ }
+ });
+ tbl_summary.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelections();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ mainFrame.dispose();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_view.isEnabled())
+ {
+ ok_ActionPerformed();
+ }
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ pnl_filter.requestFocus();
+ }
+ else
+ {
+ btn_view.requestFocus();
+ }
+ evt.consume();
+ break;
+ default:
+ return;
+ }
+ }
+ });
tbl_local_pdb.setAutoCreateRowSorter(true);
tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
tbl_local_pdb.addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
{
- updateCurrentView();
+ validateSelections();
}
public void mouseReleased(MouseEvent e)
{
- updateCurrentView();
+ validateSelections();
+ }
+ });
+ tbl_local_pdb.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelections();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ mainFrame.dispose();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_view.isEnabled())
+ {
+ ok_ActionPerformed();
+ }
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ cmb_filterOption.requestFocus();
+ }
+ else
+ {
+ if (btn_view.isEnabled())
+ {
+ btn_view.requestFocus();
+ }
+ else
+ {
+ btn_cancel.requestFocus();
+ }
+ }
+ evt.consume();
+ default:
+ return;
+ }
}
});
-
btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
btn_view.setText(MessageManager.getString("action.view"));
btn_view.addActionListener(new java.awt.event.ActionListener()
ok_ActionPerformed();
}
});
+ btn_view.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ ok_ActionPerformed();
+ }
+ }
+ });
+
btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
mainFrame.dispose();
}
});
+ btn_cancel.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ mainFrame.dispose();
+ }
+ }
+ });
btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
String btn_title = MessageManager.getString("label.select_pdb_file");
pdbFromFile_actionPerformed();
}
});
+ btn_pdbFromFile.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ }
+ });
scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
scrl_foundStructures
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.json.binding.biojson.v1;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColour;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+public class ColourSchemeMapper
+{
+ private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
+ csHelix, csTurn, csStrand, csBuried, csHydro,
+ csRNAInteractionType, csPID, csBlosum62 = null;
+ static
+ {
+ csZappo = new ZappoColourScheme();
+ csTaylor = new TaylorColourScheme();
+ csNucleotide = new NucleotideColourScheme();
+ csPurine = new PurinePyrimidineColourScheme();
+ csHelix = new HelixColourScheme();
+ csTurn = new TurnColourScheme();
+ csStrand = new StrandColourScheme();
+ csBuried = new BuriedColourScheme();
+ csHydro = new HydrophobicColourScheme();
+ csRNAInteractionType = new RNAInteractionColourScheme();
+ csPID = new PIDColourScheme();
+ csBlosum62 = new Blosum62ColourScheme();
+ }
+ public static ColourSchemeI getJalviewColourScheme(
+ String colourSchemeName, AnnotatedCollectionI annotCol)
+ {
+ switch (colourSchemeName.toUpperCase())
+ {
+ case "ZAPPO":
+ return csZappo;
+ case "TAYLOR":
+ return csTaylor;
+ case "NUCLEOTIDE":
+ return csNucleotide;
+ case "PURINE":
+ case "PURINE/PYRIMIDINE":
+ return csPurine;
+ case "HELIX":
+ case "HELIX PROPENSITY":
+ return csHelix;
+ case "TURN":
+ case "TURN PROPENSITY":
+ return csTurn;
+ case "STRAND":
+ case "STRAND PROPENSITY":
+ return csStrand;
+ case "BURIED":
+ case "BURIED INDEX":
+ return csBuried;
+ case "HYDRO":
+ case "HYDROPHOBIC":
+ return csHydro;
+ case "RNA INTERACTION TYPE":
+ return csRNAInteractionType;
+ case "PID":
+ case "% IDENTITY":
+ return csPID;
+ case "BLOSUM62":
+ return csBlosum62;
+ case "T-COFFEE SCORES":
+ return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
+ case "RNA HELICES":
+ return (annotCol != null) ? new RNAHelicesColour(annotCol) : null;
+ case "CLUSTAL":
+ return (annotCol != null) ? new ClustalxColourScheme(annotCol, null)
+ : null;
+ case "USER DEFINED":
+ return null;
+ default:
+ return null;
+ }
+ }
+}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.json.binding.biojson.v1;
-
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-public enum JalviewBioJsColorSchemeMapper
-{
-
- USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
- null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
- "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
- new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide",
- new NucleotideColourScheme()), PURINE_PYRIMIDINE(
- "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENSITY(
- "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
- "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
- "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
- "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
- "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-
- // The color types below are not yet supported by BioJs MSA viewer
- T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
- "RNA Interaction type", "RNA Interaction type",
- new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
- "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
- "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
- "% Identity", "pid", new PIDColourScheme());
-
- private String jalviewName;
-
- private String bioJsName;
-
- private ColourSchemeI jvColourScheme;
-
- private JalviewBioJsColorSchemeMapper(String jalviewName,
- String bioJsName, ColourSchemeI jvColourScheme)
- {
- this.jalviewName = jalviewName;
- this.bioJsName = bioJsName;
- this.setJvColourScheme(jvColourScheme);
- }
-
- public String getJalviewName()
- {
- return jalviewName;
- }
-
- public String getBioJsName()
- {
- return bioJsName;
- }
-
- public ColourSchemeI getJvColourScheme()
- {
- return jvColourScheme;
- }
-
- public void setJvColourScheme(ColourSchemeI jvColourScheme)
- {
- this.jvColourScheme = jvColourScheme;
- }
-
-}
package jalview.util;
import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.regex.Pattern;
return htmlContent;
}
- ArrayList<String> links = new ArrayList<String>();
+ List<String> links = new ArrayList<String>();
- StringBuffer sb = new StringBuffer();
+ String content;
/**
* result of parsing description - with or without HTML tags
public String getContent()
{
- return sb.toString();
+ return content;
}
/**
*
* @return
*/
- public ArrayList<String> getLinks()
+ public List<String> getLinks()
{
return links;
}
/**
+ * Parses the given html and
+ * <ul>
+ * <li>extracts any 'href' links to a list of "displayName|url" strings,
+ * retrievable by #getLinks</li>
+ * <li>extracts the remaining text (with %LINK% placeholders replacing hrefs),
+ * retrievable by #getContent</li>
+ * </ul>
*
* @param description
* - html or text content to be parsed
public ParseHtmlBodyAndLinks(String description, boolean removeHTML,
String newline)
{
+ StringBuilder sb = new StringBuilder(description.length());
if (description == null || description.length() == 0)
{
htmlContent = false;
String tag = null;
while (st.hasMoreElements())
{
- token = st.nextToken("&>");
+ token = st.nextToken(">");
if (token.equalsIgnoreCase("html") || token.startsWith("/"))
{
continue;
{
sb.append(newline);
}
- else if (token.startsWith("lt;"))
- {
- sb.append("<" + token.substring(3));
- }
- else if (token.startsWith("gt;"))
- {
- sb.append(">" + token.substring(3));
- }
- else if (token.startsWith("amp;"))
- {
- sb.append("&" + token.substring(4));
- }
else
{
sb.append(token);
{
// instead of parsing the html into plaintext
// clean the description ready for embedding in html
- sb = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(description)
- .replaceAll("<"));
-
+ sb = new StringBuilder(LEFT_ANGLE_BRACKET_PATTERN
+ .matcher(description).replaceAll("<"));
}
+ content = translateEntities(sb.toString());
+ }
+ private String translateEntities(String s)
+ {
+ s = s.replaceAll("&", "&");
+ s = s.replaceAll("<", "<");
+ s = s.replaceAll(">", ">");
+ return s;
}
/**
*/
public String getNonHtmlContent()
{
- return isHtmlContent() ? sb.toString() : orig;
+ return isHtmlContent() ? content : orig;
}
}
@Override
public Map<String, Object> getFeatureColours()
{
- return new ConcurrentHashMap<String, Object>(featureColours);
+ return featureColours;
}
/**
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(Alignment dataset, Map featureColours)
{
if (result != null && result.isFinished())
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Hashtable featureColours = new Hashtable();
+ Map featureColours = new HashMap();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
package jalview.ws.uimodel;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
private boolean allowEmptySequence;
+ private boolean allowUnpublishedEntries = Cache.getDefault(
+ "ALLOW_UNPUBLISHED_PDB_QUERYING", false);
+
private int responseSize;
private boolean isSortAscending;
- private Collection<PDBDocField> wantedFields;// = new
- // Collection<PDBDocField>();
+ private Collection<PDBDocField> wantedFields;
public String getFieldToSearchBy()
{
public String getQuery()
{
return fieldToSearchBy + searchTerm
- + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]");
+ + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]")
+ + (isAllowUnpublishedEntries() ? "" : " AND status:REL");
}
public String toString()
+ " isAsc: " + isAscending() + " Associated Seq : "
+ associatedSequence;
}
+
+ public boolean isAllowUnpublishedEntries()
+ {
+ return allowUnpublishedEntries;
+ }
+
+ public void setAllowUnpublishedEntries(boolean allowUnpublishedEntries)
+ {
+ this.allowUnpublishedEntries = allowUnpublishedEntries;
+ }
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.gui.AlignFrame;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class FeaturesFileTest
+{
+
+ static String TestFiles[][] = {
+ { "Test example features import/export",
+ "examples/uniref50.fa", "examples/exampleFeatures.txt" } };
+
+ @Test(groups = { "Functional" })
+ public void testParse() throws Exception
+ {
+ testFeaturesFileIO("Features file test");
+ }
+
+ public static AlignmentI readAlignmentFile(File f) throws IOException
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ FormatAdapter rf = new FormatAdapter();
+
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+
+ al.setDataset(null); // creates dataset sequences
+ assertNotNull("Couldn't read supplied alignment data.", al);
+ return al;
+ }
+
+ /**
+ * Helper method for testing
+ *
+ * @param testname
+ * @param f
+ * alignment file
+ * @param featFile
+ * features file to load on to the alignment
+ * @throws IOException
+ */
+ public static void testFeaturesFileIO(String testname) throws IOException
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, Object> colours = af.getFeatureRenderer()
+ .getFeatureColours();
+ FeaturesFile featuresFile = new FeaturesFile(
+ "examples/exampleFeatures.txt", FormatAdapter.FILE);
+ assertTrue("Test " + testname + "\nFailed to parse features file.",
+ featuresFile.parse(al.getDataset(), colours, true));
+
+ /*
+ * Refetch the colour map from the FeatureRenderer (to confirm it has been
+ * updated - JAL-1904), and verify (some) feature group colours
+ */
+ colours = af.getFeatureRenderer().getFeatureColours();
+ assertEquals("26 feature group colours not found", 26, colours.size());
+ assertEquals(colours.get("Cath"), new Color(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
+
+ /*
+ * verify (some) features on sequences
+ */
+ SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceFeatures(); // FER_CAPAA
+ assertEquals(7, sfs.length);
+ SequenceFeature sf = sfs[0];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(39, sf.begin);
+ assertEquals(39, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[1];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(44, sf.begin);
+ assertEquals(44, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[2];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(47, sf.begin);
+ assertEquals(47, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[3];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(77, sf.begin);
+ assertEquals(77, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[4];
+ assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
+ sf.description);
+ assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
+ sf.links.get(0).toString());
+ assertEquals(8, sf.begin);
+ assertEquals(83, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Pfam", sf.type);
+ sf = sfs[5];
+ assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
+ assertEquals(3, sf.begin);
+ assertEquals(93, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Cath", sf.type);
+ sf = sfs[6];
+ assertEquals(
+ "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
+ sf.description);
+ assertEquals(
+ "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
+ sf.links.get(0).toString());
+ assertEquals(89, sf.begin);
+ assertEquals(89, sf.end);
+ assertEquals("netphos", sf.featureGroup);
+ assertEquals("PHOSPHORYLATION (T)", sf.type);
+ }
+}
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ZappoColourScheme;
import java.io.IOException;
import java.util.ArrayList;
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- ColourSchemeI scheme = JSONFile.getJalviewColorScheme("zappo");
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
- scheme, true, true, false, 21, 29);
+ null, true, true, false, 21, 29);
+ ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+ "zappo", seqGrp);
+ seqGrp.cs = scheme;
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
- af.changeColour(jf.getColourScheme());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
@Test(groups = { "Functional" })
public void colorSchemeTest()
{
- Assert.assertNotNull(testJsonFile.getColourScheme(),
+ Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
"Colourscheme is null, parsing failed!");
- Assert.assertTrue(
- testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+ Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
"Zappo colour scheme expected!");
+ // Assert.assertTrue(
+ // testJsonFile.getGlobalColourScheme() instanceof ZappoColourScheme,
+ // "Zappo colour scheme expected!");
}
@Test(groups = { "Functional" })
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
+ System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
- && expectedGrp.cs.equals(actualGrp.cs)
+ && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
--- /dev/null
+package jalview.util;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class ParseHtmlBodyAndLinksTest
+{
+ @Test(groups = { "Functional" })
+ public void testParseHtml_noLinks()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>something here</html>", false, "\n");
+ assertEquals("something here", testee.getContent());
+ assertEquals("something here", testee.getNonHtmlContent());
+
+ // second argument makes no difference??
+ testee = new ParseHtmlBodyAndLinks("<html>something here</html>", true,
+ "\n");
+ assertEquals("something here", testee.getContent());
+ assertEquals("something here", testee.getNonHtmlContent());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinks()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com\">on this</a> to learn more about <a href=\"http://www.somewhere.com/here\">this</a></html>",
+ false, "\n");
+ assertEquals(
+ "Please click on this%LINK% to learn more about this%LINK%",
+ testee.getContent());
+ assertEquals(
+ "Please click on this%LINK% to learn more about this%LINK%",
+ testee.getNonHtmlContent());
+ assertEquals(2, testee.getLinks().size());
+ assertEquals("on this|http://www.nowhere.com", testee.getLinks().get(0));
+ assertEquals("this|http://www.somewhere.com/here", testee.getLinks()
+ .get(1));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinksWithParameters()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com?id=234&taxon=human\">on this</a> to learn more</html>",
+ false, "\n");
+ assertEquals("Please click on this%LINK% to learn more",
+ testee.getContent());
+ assertEquals("Please click on this%LINK% to learn more",
+ testee.getNonHtmlContent());
+ assertEquals(1, testee.getLinks().size());
+ assertEquals("on this|http://www.nowhere.com?id=234&taxon=human",
+ testee.getLinks().get(0));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinksWithEncoding()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com?id=234&taxon=human&id>3&id<10\">on this</a> to learn &<>more</html>",
+ false, "\n");
+ // html encoding in the text body is translated
+ assertEquals("Please click on this%LINK% to learn &<>more",
+ testee.getContent());
+ assertEquals("Please click on this%LINK% to learn &<>more",
+ testee.getNonHtmlContent());
+ assertEquals(1, testee.getLinks().size());
+ // html encoding in the url links is not translated
+ assertEquals(
+ "on this|http://www.nowhere.com?id=234&taxon=human&id>3&id<10",
+ testee.getLinks().get(0));
+ }
+}
if (pdbJsonDoc.get(field.getCode()) == null)
{
// System.out.println(">>>\t" + field.getCode());
- assertTrue(field.getClass()
+ assertTrue(field.getCode()
+ " has been removed from PDB doc Entity",
!pdbJsonResponseString.contains(field.getCode()));
}
git://source.jalview.org / jalview.git / commitdiff