/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
+import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
}
}
- if (jdatasq.getPDBId() != null)
+ if (jdatasq.getAllPDBEntries() != null)
{
- Enumeration en = jdatasq.getPDBId().elements();
+ Enumeration en = jdatasq.getAllPDBEntries().elements();
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
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);
view.setFontName(av.font.getName());
view.setFontSize(av.font.getSize());
view.setFontStyle(av.font.getStyle());
+ view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
view.setRenderGaps(av.isRenderGaps());
view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
+ if (Desktop.desktop == null)
+ {
+ return;
+ }
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
}
}
throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam", new Object[]
- { calcIdParam.toString() }));
+ "error.unsupported_version_calcIdparam",
+ new Object[] { calcIdParam.toString() }));
}
/**
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);
/*
else
{
// defer to later
- frefedSequence.add(new Object[]
- { maps[m].getDnasq(), cf, mapping });
+ frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+ mapping });
}
}
}
* indicate that annotation colours are applied across all groups (pre
* Jalview 2.8.1 behaviour)
*/
- boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
- object.getVersion());
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
+ "2.8.1", object.getVersion());
AlignmentPanel ap = null;
boolean isnewview = true;
newFileLoc.append(";");
}
- if (newFileLoc.length() > 0)
+ if (newFileLoc.length() == 0)
+ {
+ return;
+ }
+ int histbug = newFileLoc.indexOf("history = ");
+ if (histbug > -1)
{
- int histbug = newFileLoc.indexOf("history = ");
+ /*
+ * change "history = [true|false];" to "history = [1|0];"
+ */
histbug += 10;
int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
String val = (diff == -1) ? null : newFileLoc
.substring(histbug, diff);
if (val != null && val.length() >= 4)
{
- if (val.contains("e"))
+ if (val.contains("e")) // eh? what can it be?
{
if (val.trim().equals("true"))
{
newFileLoc.replace(histbug, diff, val);
}
}
+ }
- final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
- .size()]);
- final String[] id = pdbids.toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = seqmaps
- .toArray(new SequenceI[seqmaps.size()][]);
- final String fileloc = newFileLoc.toString();
- final String sviewid = viewerData.getKey();
- final AlignFrame alf = af;
- final Rectangle rect = new Rectangle(svattrib.getX(),
- svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
- try
+ final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+ .size()]);
+ final String[] id = pdbids.toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString();
+ final String sviewid = viewerData.getKey();
+ final AlignFrame alf = af;
+ final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
+ svattrib.getWidth(), svattrib.getHeight());
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
{
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ JalviewStructureDisplayI sview = null;
+ try
{
- JalviewStructureDisplayI sview = null;
- try
- {
- sview = new StructureViewer(alf.alignPanel
- .getStructureSelectionManager()).createView(
- StructureViewer.ViewerType.JMOL, pdbf, id, sq,
- alf.alignPanel, svattrib, fileloc, rect, sviewid);
- addNewStructureViewer(sview);
- } catch (OutOfMemoryError ex)
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
{
- new OOMWarning("restoring structure view for PDB id " + id,
- (OutOfMemoryError) ex.getCause());
- if (sview != null && sview.isVisible())
- {
- sview.closeViewer(false);
- sview.setVisible(false);
- sview.dispose();
- }
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
}
}
- });
- } catch (InvocationTargetException ex)
- {
- warn("Unexpected error when opening Jmol view.", ex);
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
}
+
}
/**
* @return true if version is development/null or evaluates to the same or
* later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
*/
- protected boolean isVersionStringLaterThan(String supported,
+ public static boolean isVersionStringLaterThan(String supported,
String version)
{
if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
try
{
- if (Float.valueOf(curT) > Float.valueOf(fileT))
+ float supportedVersionToken = Float.parseFloat(curT);
+ float myVersiontoken = Float.parseFloat(fileT);
+ if (supportedVersionToken > myVersiontoken)
{
// current version is newer than the version that wrote the file
return false;
}
+ if (supportedVersionToken < myVersiontoken)
+ {
+ // current version is older than the version that wrote the file
+ return true;
+ }
} catch (NumberFormatException nfe)
{
System.err
af.viewport.setFont(
new java.awt.Font(view.getFontName(), view.getFontStyle(), view
.getFontSize()), true);
+ ViewStyleI vs = af.viewport.getViewStyle();
+ vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
+ af.viewport.setViewStyle(vs);
// TODO: allow custom charWidth/Heights to be restored by updating them
// after setting font - which means set above to false
af.viewport.setRenderGaps(view.getRenderGaps());
/**
* Kludge for magic autoannotation names (see JAL-811)
*/
- String[] magicNames = new String[]
- { "Consensus", "Quality", "Conservation" };
+ String[] magicNames = new String[] { "Consensus", "Quality",
+ "Conservation" };
JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
for (String nm : magicNames)
}
else
{
- frefedSequence.add(new Object[]
- { dsfor, jmap });
+ frefedSequence.add(new Object[] { dsfor, jmap });
}
}
else
git://source.jalview.org / jalview.git / blobdiff