<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
- <em>6/10/2015</em></strong>
+ <em>8/10/2015</em></strong>
</div>
</td>
<td>
* @param cdnaAlignment
* @return
*/
- public static boolean mapProteinAlignmentToCdna(final AlignmentI proteinAlignment,
- final AlignmentI cdnaAlignment)
+ public static boolean mapProteinAlignmentToCdna(
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
{
{
return null;
}
- if (!translatesAs(cdnaSeqChars, startOffset,
- aaSeqChars))
+ if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
{
return null;
}
infoPanel
.add(new Label(MessageManager.getString("warn.delete_all")));
- final JVDialog dialog = new JVDialog(this, title, true, 400,
- 200);
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
dialog.setMainPanel(infoPanel);
dialog.ok.setLabel(MessageManager.getString("action.ok"));
dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + f + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
- while (alignedBases < truePos
- && alignedColumn < alignedSeq.length)
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
if (alignedSeq[alignedColumn++] != gap)
{
}
}
-
/**
* DOCUMENT ME!
*
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
*/
public static AlignFrame[] getAlignFrames()
{
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { currentAlignFrame };
+ }
+
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
AlignmentExportData exportData = jalview.gui.AlignFrame
.getAlignmentForExport(JSONFile.FILE_DESC,
ap.getAlignViewport(), exportSettings);
- String bioJSON = new FormatAdapter(ap,
- exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC, exportData
+ .getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap
+ .getAlignViewport().getColumnSelection());
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll("#sequenceData#", bioJSON)
- .toString();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Map colours,
- boolean removeHTML)
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
{
return parse(align, colours, null, removeHTML, false);
}
seqMap.put(seqUniqueId, seq);
}
-
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
- displayBoxes, displayText, colourText,
- startRes, endRes);
+ displayBoxes, displayText, colourText, startRes, endRes);
seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
import java.util.ArrayList;
import java.util.List;
{
if (btn_view.isEnabled())
{
- btn_view.requestFocus();
+ btn_view.requestFocus();
}
else
{
csPID = new PIDColourScheme();
csBlosum62 = new Blosum62ColourScheme();
}
+
public static ColourSchemeI getJalviewColourScheme(
String colourSchemeName, AnnotatedCollectionI annotCol)
{
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[] {
- sequenceStart + absStart,
- sequenceStart + absStart + entrySeq.length() - 1 },
- new int[] { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null, new int[] { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+ { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end
}
*/
package jalview.ws.uimodel;
-
public class AlignAnalysisUIText
{