X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=64d00ffef113a5396165b52f39ae19f7a55659f7;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=393b1927a748ea367f27b6e372f4d54e9a98bd18;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 393b192..64d00ff 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,481 +1,468 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 .
*/
package jalview.gui;
-import jalview.schemes.*;
-
import java.io.*;
-
import java.net.*;
-
import java.util.*;
-
import java.util.jar.*;
import javax.swing.*;
import org.exolab.castor.xml.*;
-
import jalview.binding.*;
-
-
-
+import jalview.schemes.*;
+import jalview.util.jarInputStreamProvider;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class Jalview2XML_V1
{
- jalview.schemes.UserColourScheme GetUserColourScheme(
- JalviewModelSequence jms, String id)
- {
- UserColours[] uc = jms.getUserColours();
- UserColours colours = null;
+ boolean raiseGUI = true;
- for (int i = 0; i < uc.length; i++)
- {
- if (uc[i].getId().equals(id))
- {
- colours = uc[i];
+ public Jalview2XML_V1()
+ {
- break;
- }
- }
+ };
- int csize = colours.getUserColourScheme().getColourCount();
- java.awt.Color[] newColours = new java.awt.Color[csize];
+ public Jalview2XML_V1(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ };
- for (int i = 0; i < csize; i++)
- {
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i).getRGB(), 16));
- }
+ jalview.schemes.UserColourScheme GetUserColourScheme(
+ JalviewModelSequence jms, String id)
+ {
+ UserColours[] uc = jms.getUserColours();
+ UserColours colours = null;
+
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
- return new jalview.schemes.UserColourScheme(newColours);
+ break;
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- */
- public AlignFrame LoadJalviewAlign(final String file)
+ int csize = colours.getUserColourScheme().getColourCount();
+ java.awt.Color[] newColours = new java.awt.Color[csize];
+
+ for (int i = 0; i < csize; i++)
{
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i).getRGB(), 16));
+ }
- jalview.gui.AlignFrame af = null;
+ return new jalview.schemes.UserColourScheme(newColours);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file
+ * DOCUMENT ME!
+ */
+ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ final String file = jprovider.getFilename();
+ jalview.gui.AlignFrame af = null;
+
+ try
+ {
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
- try
+ do
+ {
+ jin = jprovider.getJarInputStream();
+
+ for (int i = 0; i < entryCount; i++)
{
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- URL url = null;
-
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
-
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
-
- do
- {
- if (url != null)
- {
- jin = new JarInputStream(url.openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
-
- for (int i = 0; i < entryCount; i++)
- {
- jarentry = jin.getNextJarEntry();
- }
-
- class NoDescIDResolver implements IDResolver
- {
- public Object resolve(String idref)
- {
- System.out.println(idref+" used");
- return null;
- }
- }
-
-
- if (jarentry != null)
- {
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
- JalviewModel object = new JalviewModel();
-
- object = (JalviewModel) object.unmarshal(in);
-
- af = LoadFromObject(object, file);
- entryCount++;
- }
- }
- while (jarentry != null);
+ jarentry = jin.getNextJarEntry();
}
- catch (final java.net.UnknownHostException ex)
+
+ class NoDescIDResolver implements IDResolver
{
- ex.printStackTrace();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ public Object resolve(String idref)
{
- public void run()
- {
-
- System.err.println("Couldn't locate Jalview XML file : " +
- ex + "\n");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
- }
- });
+ System.out.println(idref + " used");
+ return null;
+ }
}
- catch (Exception ex)
+
+ if (jarentry != null)
{
- ex.printStackTrace();
- System.err.println("Exception whilst loading jalview XML file : " +
- ex + "\n");
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+ JalviewModel object = new JalviewModel();
+
+ object = (JalviewModel) object.unmarshal(in);
+
+ af = LoadFromObject(object, file);
+ entryCount++;
+ }
+ } while (jarentry != null);
+ } catch (final java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
{
- public void run()
- {
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file,
- "Error loading Jalview file",
- JOptionPane.WARNING_MESSAGE);
- }
- });
+
+ System.err.println("Couldn't locate Jalview XML file : " + ex
+ + "\n");
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + file, "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ ;
+ } catch (Exception ex)
+ {
+ System.err.println("Exception whilst loading jalview XML file : ");
+ ex.printStackTrace();
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error loading " + file, "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ }
+
+ return af;
+ }
+
+ AlignFrame LoadFromObject(JalviewModel object, String file)
+ {
+ Vector seqids = new Vector();
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+ Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+ JalviewModelSequence jms = object.getJalviewModelSequence();
+
+ // ////////////////////////////////
+ // LOAD SEQUENCES
+ jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+ vamsasSeq[i].getSequence());
+ jseqs[i].setStart(JSEQ[i].getStart());
+ jseqs[i].setEnd(JSEQ[i].getEnd());
+ seqids.add(jseqs[i]);
+ }
+
+ // /SequenceFeatures are added to the DatasetSequence,
+ // so we must create the dataset before loading features
+ // ///////////////////////////////
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+ al.setDataset(null);
+ // ///////////////////////////////
+
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ if (JSEQ[i].getFeaturesCount() > 0)
+ {
+ Features[] features = JSEQ[i].getFeatures();
+ for (int f = 0; f < features.length; f++)
+ {
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+ features[f].getType(), features[f].getDescription(),
+ features[f].getStatus(), features[f].getBegin(),
+ features[f].getEnd(), null);
+
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ }
+ }
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+ entry.setId(ids[p].getId());
+ entry.setType(ids[p].getType());
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
- return af;
+ }
}
- AlignFrame LoadFromObject(JalviewModel object, String file)
+ // ///////////////////////////////
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ if (vamsasSet.getAnnotation() != null)
{
- Vector seqids = new Vector();
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
- Sequence[] vamsasSeq = vamsasSet.getSequence();
+ Annotation[] an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.length; i++)
+ {
+ AnnotationElement[] ae = an[i].getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
+ .getWidth()];
- JalviewModelSequence jms = object.getJalviewModelSequence();
+ for (int aa = 0; aa < ae.length; aa++)
+ {
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue());
+ }
- //////////////////////////////////
- //LOAD SEQUENCES
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
- for (int i = 0; i < vamsasSeq.length; i++)
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (an[i].getGraph())
{
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseqs[i].setStart(JSEQ[i].getStart());
- jseqs[i].setEnd(JSEQ[i].getEnd());
- seqids.add(jseqs[i]);
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot, 0, 0,
+ jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
}
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot);
+ }
+
+ al.addAnnotation(jaa);
+ }
+ }
+
+ // ///////////////////////////////
+ // LOAD VIEWPORT
+ Viewport[] views = jms.getViewport();
+ Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+ AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
+ }
- ///SequenceFeatures are added to the DatasetSequence,
- // so we must create the dataset before loading features
- /////////////////////////////////
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
- al.setDataset(null);
- /////////////////////////////////
+ // af.changeColour() );
+ // ///////////////////////
+ // LOAD GROUPS
+ if (jms.getJGroupCount() > 0)
+ {
+ JGroup[] groups = jms.getJGroup();
+
+ for (int i = 0; i < groups.length; i++)
+ {
+ ColourSchemeI cs = null;
- for (int i = 0; i < vamsasSeq.length; i++)
+ if (groups[i].getColour() != null)
{
- if (JSEQ[i].getFeaturesCount() > 0)
+ if (groups[i].getColour().startsWith("ucs"))
{
- Features[] features = JSEQ[i].getFeatures();
- for (int f = 0; f < features.length; f++)
- {
- jalview.datamodel.SequenceFeature sf
- = new jalview.datamodel.SequenceFeature(features[f].getType(),
- features[f].getDescription(), features[f].getStatus(),
- features[f].getBegin(), features[f].getEnd(),
- null);
-
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
- }
+ cs = GetUserColourScheme(jms, groups[i].getColour());
}
- if (JSEQ[i].getPdbidsCount() > 0)
+ else
{
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
- {
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(ids[p].getId());
- entry.setType(ids[p].getType());
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
- }
+ cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+ }
+ if (cs != null)
+ {
+ cs.setThreshold(groups[i].getPidThreshold(), true);
}
- }
- /////////////////////////////////
- //////////////////////////////////
- //LOAD ANNOTATIONS
- if (vamsasSet.getAnnotation() != null)
- {
- Annotation[] an = vamsasSet.getAnnotation();
-
- for (int i = 0; i < an.length; i++)
- {
- AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
-
- for (int aa = 0; aa < ae.length; aa++)
- {
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
- ae[aa].getDescription(),
- ae[aa].getSecondaryStructure().charAt(0),
- ae[aa].getValue());
- }
-
- jalview.datamodel.AlignmentAnnotation jaa = null;
-
- if (an[i].getGraph())
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0,
- jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
- }
- else
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
- }
-
- al.addAnnotation(jaa);
- }
}
+ Vector seqs = new Vector();
+ int[] ids = groups[i].getSeq();
- /////////////////////////////////
- // LOAD VIEWPORT
- Viewport[] views = jms.getViewport();
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+ for (int s = 0; s < ids.length; s++)
+ {
+ seqs.addElement((jalview.datamodel.SequenceI) seqids
+ .elementAt(ids[s]));
+ }
- AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
+ seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+ groups[i].getDisplayText(), groups[i].getColourText(),
+ groups[i].getStart(), groups[i].getEnd());
- af.setFileName(file, "Jalview");
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
- for (int i = 0; i < JSEQ.length; i++)
+ if (groups[i].getConsThreshold() != 0)
{
- af.viewport.setSequenceColour(
- af.viewport.alignment.getSequenceAt(i),
- new java.awt.Color(
- JSEQ[i].getColour()));
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+ "All", ResidueProperties.propHash, 3,
+ sg.getSequences(null), 0, sg.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, 25);
+ sg.cs.setConservation(c);
}
+ al.addGroup(sg);
+ }
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setColourText(view.getShowColourText());
+ af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setShowJVSuffix(view.getShowFullId());
+ af.viewport.setFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), view.getFontSize()));
+ af.alignPanel.fontChanged();
+
+ af.viewport.setRenderGaps(view.getRenderGaps());
+ af.viewport.setWrapAlignment(view.getWrapAlignment());
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+ af.viewport.setShowBoxes(view.getShowBoxes());
+ af.viewport.setShowText(view.getShowText());
+
+ ColourSchemeI cs = null;
+
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, view.getBgColour());
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ }
+
+ if (cs != null)
+ {
+ cs.setThreshold(view.getPidThreshold(), true);
+ cs.setConsensus(af.viewport.hconsensus);
+ }
+ }
- // af.changeColour() );
- /////////////////////////
- //LOAD GROUPS
- if (jms.getJGroupCount() > 0)
- {
- JGroup[] groups = jms.getJGroup();
-
- for (int i = 0; i < groups.length; i++)
- {
- ColourSchemeI cs = null;
-
- if (groups[i].getColour() != null)
- {
- if (groups[i].getColour().startsWith("ucs"))
- {
- cs = GetUserColourScheme(jms, groups[i].getColour());
- }
- else
- {
- cs = ColourSchemeProperty.getColour(al,
- groups[i].getColour());
- }
-
- if(cs!=null)
- cs.setThreshold(groups[i].getPidThreshold(), true);
-
- }
-
- Vector seqs = new Vector();
- int[] ids = groups[i].getSeq();
-
- for (int s = 0; s < ids.length; s++)
- {
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
- ids[s]));
- }
-
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),
- groups[i].getDisplayText(), groups[i].getColourText(),
- groups[i].getStart(), groups[i].getEnd());
-
- sg.setOutlineColour(new java.awt.Color(
- groups[i].getOutlineColour()));
-
- if (groups[i].getConsThreshold() != 0)
- {
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
- ResidueProperties.propHash, 3, sg.getSequences(null), 0,
- sg.getWidth() - 1);
- c.calculate();
- c.verdict(false, 25);
- sg.cs.setConservation(c);
- }
-
- al.addGroup(sg);
- }
- }
+ af.viewport.setGlobalColourScheme(cs);
+ af.viewport.setColourAppliesToAllGroups(false);
+ af.changeColour(cs);
+ if (view.getConservationSelected() && cs != null)
+ {
+ cs.setConservationInc(view.getConsThreshold());
+ }
+ af.viewport.setColourAppliesToAllGroups(true);
+ af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+ if (jms.getFeatureSettings() != null)
+ {
+ af.viewport.featuresDisplayed = new Hashtable();
+ String[] renderOrder = new String[jms.getFeatureSettings()
+ .getSettingCount()];
+ for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ {
+ Setting setting = jms.getFeatureSettings().getSetting(fs);
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.viewport.setAbovePIDThreshold(view.getPidSelected());
- af.viewport.setColourText(view.getShowColourText());
- af.viewport.setConservationSelected(view.getConservationSelected());
- af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.setFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
-
- af.viewport.setRenderGaps(view.getRenderGaps());
- af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
- af.viewport.setShowBoxes(view.getShowBoxes());
- af.viewport.setShowText(view.getShowText());
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), new java.awt.Color(setting.getColour()));
- ColourSchemeI cs = null;
+ renderOrder[fs] = setting.getType();
- if (view.getBgColour() != null)
+ if (setting.getDisplay())
{
- if (view.getBgColour().startsWith("ucs"))
- {
- cs = GetUserColourScheme(jms, view.getBgColour());
- }
- else
- {
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
- }
-
- if(cs!=null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
- }
+ af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ setting.getColour()));
}
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ }
+
+ af.setMenusFromViewport(af.viewport);
+
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.setColourAppliesToAllGroups(false);
- af.changeColour(cs);
- if (view.getConservationSelected() && cs!=null)
+ // LOAD TREES
+ // /////////////////////////////////////
+ if (jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
{
- cs.setConservationInc(view.getConsThreshold());
- }
- af.viewport.setColourAppliesToAllGroups(true);
- af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+ Tree tree = jms.getTree(t);
+ TreePanel tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
- if(jms.getFeatureSettings()!=null)
- {
- af.viewport.featuresDisplayed = new Hashtable();
- String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
- for(int fs=0; fs 0)
- {
- try
- {
- for (int t = 0; t < jms.getTreeCount(); t++)
- {
-
- Tree tree = jms.getTree(t);
-
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
- tree.getNewick()), tree.getTitle(),
- tree.getWidth(), tree.getHeight(),
- tree.getXpos(), tree.getYpos());
-
- tp.fitToWindow.setState(tree.getFitToWindow());
- tp.fitToWindow_actionPerformed(null);
-
- if(tree.getFontName()!=null)
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),
- tree.getFontStyle(),
- tree.getFontSize()));
- else
- tp.setTreeFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(),
- tree.getFontSize()));
-
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
-
- tp.treeCanvas.threshold = tree.getThreshold();
-
- if (tree.getCurrentTree())
- af.viewport.setCurrentTree(tp.getTree());
- }
-
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ tp.treeCanvas.threshold = tree.getThreshold();
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
}
- return af;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
}
-}
+ return af;
+ }
+}