*/
package jalview.gui;
-import java.awt.Rectangle;
-import java.io.*;
-import java.lang.reflect.InvocationTargetException;
-import java.net.*;
-import java.util.*;
-import java.util.Map.Entry;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.schemabinding.version2.*;
-import jalview.schemes.*;
+import jalview.schemabinding.version2.AlcodMap;
+import jalview.schemabinding.version2.Alcodon;
+import jalview.schemabinding.version2.AlcodonFrame;
+import jalview.schemabinding.version2.Annotation;
+import jalview.schemabinding.version2.AnnotationColours;
+import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.CalcIdParam;
+import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.Features;
+import jalview.schemabinding.version2.Group;
+import jalview.schemabinding.version2.HiddenColumns;
+import jalview.schemabinding.version2.JGroup;
+import jalview.schemabinding.version2.JSeq;
+import jalview.schemabinding.version2.JalviewModel;
+import jalview.schemabinding.version2.JalviewModelSequence;
+import jalview.schemabinding.version2.MapListFrom;
+import jalview.schemabinding.version2.MapListTo;
+import jalview.schemabinding.version2.Mapping;
+import jalview.schemabinding.version2.MappingChoice;
+import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PdbentryItem;
+import jalview.schemabinding.version2.Pdbids;
+import jalview.schemabinding.version2.Property;
+import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequenceSet;
+import jalview.schemabinding.version2.SequenceSetProperties;
+import jalview.schemabinding.version2.Setting;
+import jalview.schemabinding.version2.StructureState;
+import jalview.schemabinding.version2.ThresholdLine;
+import jalview.schemabinding.version2.Tree;
+import jalview.schemabinding.version2.UserColours;
+import jalview.schemabinding.version2.Viewport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Unmarshaller;
+
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for " + _af.getTitle();
+ String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
.startsWith(
jmol.jmb.pdbentry[peid].getId()
.toLowerCase())))
+ {
continue;
+ }
if (matchedFile == null)
{
matchedFile = jmol.jmb.pdbentry[peid].getFile();
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
AnnotationElement ae;
if (aa[i].annotations != null)
ae = new AnnotationElement();
if (aa[i].annotations[a].description != null)
+ {
ae.setDescription(aa[i].annotations[a].description);
+ }
if (aa[i].annotations[a].displayCharacter != null)
+ {
ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ }
if (!Float.isNaN(aa[i].annotations[a].value))
+ {
ae.setValue(aa[i].annotations[a].value);
+ }
ae.setPosition(a);
if (aa[i].annotations[a].secondaryStructure != ' '
&& aa[i].annotations[a].secondaryStructure != '\0')
+ {
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
+ }
if (aa[i].annotations[a].colour != null
&& aa[i].annotations[a].colour != java.awt.Color.black)
return false;
}
}
- throw new Error("Unsupported Version for calcIdparam "
- + calcIdParam.toString());
+ throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
}
/**
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector<AppJmol>();
+ newStructureViewers = new Vector<JalviewStructureDisplayI>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
errorMessage = null;
}
- Hashtable alreadyLoadedPDB;
+ Hashtable<String, String> alreadyLoadedPDB;
/**
* when set, local views will be updated from view stored in JalviewXML
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
if (alreadyLoadedPDB == null)
+ {
alreadyLoadedPDB = new Hashtable();
+ }
if (alreadyLoadedPDB.containsKey(pdbId))
+ {
return alreadyLoadedPDB.get(pdbId).toString();
+ }
try
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
-
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance)
+ .registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
// in principle Visible should always be true for annotation displayed
// in multiple views
if (an[i].hasVisible())
+ {
jda.visible = an[i].getVisible();
+ }
al.addAnnotation(jda);
anpos = ae[aa].getPosition();
if (anpos >= anot.length)
+ {
continue;
+ }
anot[anpos] = new jalview.datamodel.Annotation(
jaa.setScore(an[i].getScore());
}
if (an[i].hasVisible())
+ {
jaa.visible = an[i].getVisible();
+ }
if (an[i].hasCentreColLabels())
+ {
jaa.centreColLabels = an[i].getCentreColLabels();
+ }
if (an[i].hasScaleColLabels())
{
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
-
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
@Override
public void run()
{
- AppJmol sview = null;
+ JalviewStructureDisplayI sview = null;
try
{
- sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+ sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel,
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
addNewStructureViewer(sview);
return true;
}
- Vector<AppJmol> newStructureViewers = null;
+ Vector<JalviewStructureDisplayI> newStructureViewers = null;
- protected void addNewStructureViewer(AppJmol sview)
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
{
if (newStructureViewers != null)
{
- sview.jmb.setFinishedLoadingFromArchive(false);
+ sview.getBinding().setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
{
if (newStructureViewers != null)
{
- for (AppJmol sview : newStructureViewers)
+ for (JalviewStructureDisplayI sview : newStructureViewers)
{
- sview.jmb.setFinishedLoadingFromArchive(true);
+ sview.getBinding().setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
newStructureViewers = null;
}
}
else
+ {
Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
}
}
{
skipList = skipList2;
}
-
}
git://source.jalview.org / jalview.git / blobdiff