import java.awt.Rectangle;
import java.io.*;
+import java.lang.reflect.InvocationTargetException;
import java.net.*;
import java.util.*;
import java.util.jar.*;
{
if (frames[f] instanceof AppJmol)
{
+ // TODO: revise schema to allow many:one PDB id binding to viewer
jmol = (AppJmol) frames[f];
- if (!jmol.pdbentry.getId().equals(entry.getId())
+ if (!jmol.jmb.pdbentry[0].getId().equals(entry.getId())
&& !(entry.getId().length() > 4 && entry.getId()
.toLowerCase().startsWith(
- jmol.pdbentry.getId().toLowerCase())))
+ jmol.jmb.pdbentry[0].getId().toLowerCase())))
continue;
- matchedFile = jmol.pdbentry.getFile(); // record the file so we
+ matchedFile = jmol.jmb.pdbentry[0].getFile(); // record the file so we
// can get at it if the ID
// match is ambiguous (e.g.
// 1QIP==1qipA)
state.setWidth(jmol.getWidth());
state.setHeight(jmol.getHeight());
state.setViewId(jmol.getViewId());
- String statestring = jmol.viewer.getStateInfo();
+ String statestring = jmol.jmb.viewer.getStateInfo();
if (state != null)
{
state.setContent(statestring.replaceAll("\n", ""));
}
- for (int s = 0; s < jmol.sequence.length; s++)
+ for (int s = 0; s < jmol.jmb.sequence.length; s++)
{
- if (jal.findIndex(jmol.sequence[s]) > -1)
+ if (jal.findIndex(jmol.jmb.sequence[s]) > -1)
{
pdb.addStructureState(state);
}
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
- groups[i].setShowUnconserved(sg.getShowunconserved());
+ groups[i].setShowUnconserved(sg.getShowNonconserved());
groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
// newer files have an 'autoCalculated' flag and store calculation
// state in viewport properties
jaa.autoCalculated = true; // means annotation will be marked for
- // update at end of load.
+ // update at end of load.
}
al.addAnnotation(jaa);
}
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
- sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i]
+ sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
.isShowUnconserved() : false);
sg.thresholdTextColour = groups[i].getTextColThreshold();
if (groups[i].hasShowConsensusHistogram())
;
if (groups[i].hasShowSequenceLogo())
{
- sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
+ sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
}
if (groups[i].hasIgnoreGapsinConsensus())
{
// create a new Jmol window
String state = ids[p].getStructureState(s).getContent();
StringBuffer newFileLoc = null;
- if (state.indexOf("load") > -1)
+ int cp=0;
+ if ((cp=state.indexOf("load ")) > -1)
{
- newFileLoc = new StringBuffer(state.substring(0, state
- .indexOf("\"", state.indexOf("load")) + 1));
+ newFileLoc = new StringBuffer(state.substring(0, (cp=state
+ .indexOf("\"", cp+1)+1)));
newFileLoc.append(jpdb.getFile());
newFileLoc.append(state.substring(state.indexOf("\"",
- state.indexOf("load \"") + 6)));
+ cp+1)));
}
else
{
if (newFileLoc != null)
{
- new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
- newFileLoc.toString(), new java.awt.Rectangle(x,
- y, width, height), sviewid);
+ int histbug = newFileLoc.indexOf("history = ");
+ 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.trim().equals("true")) {
+ val = "1";
+ } else {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
+ final String pdbf=pdbFile, id=ids[p].getId(), fileloc=newFileLoc.toString(),vid=sviewid;
+ final SequenceI[] sq=seq;
+ final AlignFrame alf = af;
+ final java.awt.Rectangle rect = new java.awt.Rectangle(x,
+ y, width, height);
+ try {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ new AppJmol(pdbf, id, sq, alf.alignPanel,
+ fileloc, rect, vid);
+ }
+ });
+ }
+ catch (InvocationTargetException ex)
+ {
+ System.err.println("Unexpected error when opening Jmol view.");
+ ex.printStackTrace();
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
}
}
.setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
- ((AppJmol) comp).addSequence(seq);
+ ((AppJmol) comp).jmb.addSequence(seq);
}
}
}
else if (view.getBgColour().startsWith("Annotation"))
{
// int find annotation
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ if (af.viewport.alignment.getAlignmentAnnotation() != null)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
+ for (int i = 0; i < af.viewport.alignment
+ .getAlignmentAnnotation().length; i++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i]
- .getThreshold() == null)
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ .equals(view.getAnnotationColours().getAnnotation()))
{
- af.viewport.alignment.getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
+ if (af.viewport.alignment.getAlignmentAnnotation()[i]
+ .getThreshold() == null)
+ {
+ af.viewport.alignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(view
+ .getAnnotationColours().getThreshold(),
+ "Threshold", java.awt.Color.black)
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], new java.awt.Color(view
- .getAnnotationColours().getMinColour()),
- new java.awt.Color(view.getAnnotationColours()
- .getMaxColour()), view.getAnnotationColours()
- .getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], GetUserColourScheme(
- jms, view.getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], ColourSchemeProperty
- .getColour(al, view.getAnnotationColours()
- .getColourScheme()), view
- .getAnnotationColours().getAboveThreshold());
- }
+ );
+ }
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
+ if (view.getAnnotationColours().getColourScheme().equals(
+ "None"))
{
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
- .getGroups().elementAt(g);
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], new java.awt.Color(
+ view.getAnnotationColours().getMinColour()),
+ new java.awt.Color(view.getAnnotationColours()
+ .getMaxColour()), view
+ .getAnnotationColours().getAboveThreshold());
+ }
+ else if (view.getAnnotationColours().getColourScheme()
+ .startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i],
+ GetUserColourScheme(jms, view
+ .getAnnotationColours().getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], ColourSchemeProperty
+ .getColour(al, view.getAnnotationColours()
+ .getColourScheme()), view
+ .getAnnotationColours().getAboveThreshold());
+ }
- if (sg.cs == null)
+ // Also use these settings for all the groups
+ if (al.getGroups() != null)
+ {
+ for (int g = 0; g < al.getGroups().size(); g++)
{
- continue;
- }
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+ .getGroups().elementAt(g);
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None"
- * )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.alignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours(). getMinColour()),
- * new java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- }
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /*
+ * if
+ * (view.getAnnotationColours().getColourScheme().equals("None"
+ * )) { sg.cs = new AnnotationColourGradient(
+ * af.viewport.alignment.getAlignmentAnnotation()[i], new
+ * java.awt.Color(view.getAnnotationColours().
+ * getMinColour()), new
+ * java.awt.Color(view.getAnnotationColours().
+ * getMaxColour()),
+ * view.getAnnotationColours().getAboveThreshold()); } else
+ */
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs, view.getAnnotationColours()
+ .getAboveThreshold());
+ }
+ }
}
+
+ break;
}
- break;
}
-
}
}
else
}
if (view.hasShowSequenceLogo())
{
- af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+ af.viewport.showSequenceLogo = view.getShowSequenceLogo();
}
else
{
- af.viewport.setShowSequenceLogo(false);
+ af.viewport.showSequenceLogo = false;
}
if (view.hasShowDbRefTooltip())
{
}
af.setMenusFromViewport(af.viewport);
- af.alignPanel.updateAnnotation(false); // recompute any autoannotation
// TODO: we don't need to do this if the viewport is aready visible.
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
.getHeight());
git://source.jalview.org / jalview.git / blobdiff