X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;fp=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b153d9fb5dd518c1f8ffa4f511166c38c8b64a91;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=9285754c7ca911a86ff54cbd9a4f3d816dcbcda1;hpb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
similarity index 79%
rename from src/jalview/gui/Jalview2XML.java
rename to src/jalview/project/Jalview2XML.java
index 9285754..b153d9f 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -18,7 +18,7 @@
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.gui;
+package jalview.project;
import jalview.analysis.Conservation;
import jalview.api.FeatureColourI;
@@ -42,50 +42,25 @@ import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.ext.varna.RnaModel;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.AppVarna;
+import jalview.gui.ChimeraViewFrame;
+import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.JvOptionPane;
+import jalview.gui.OOMWarning;
+import jalview.gui.PaintRefresher;
+import jalview.gui.SplitFrame;
+import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.StructureViewerBase;
+import jalview.gui.TreePanel;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.NewickFile;
import jalview.renderer.ResidueShaderI;
-import jalview.schemabinding.version2.AlcodMap;
-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.Colour;
-import jalview.schemabinding.version2.CompoundMatcher;
-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.MatchCondition;
-import jalview.schemabinding.version2.MatcherSet;
-import jalview.schemabinding.version2.OtherData;
-import jalview.schemabinding.version2.PdbentryItem;
-import jalview.schemabinding.version2.Pdbids;
-import jalview.schemabinding.version2.Property;
-import jalview.schemabinding.version2.RnaViewer;
-import jalview.schemabinding.version2.SecondaryStructure;
-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.schemabinding.version2.types.ColourThreshTypeType;
-import jalview.schemabinding.version2.types.FeatureMatcherByType;
-import jalview.schemabinding.version2.types.NoValueColour;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
@@ -110,8 +85,48 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import jalview.xml.binding.jalview.AlcodonFrame;
+import jalview.xml.binding.jalview.AlcodonFrame.AlcodMap;
+import jalview.xml.binding.jalview.Annotation;
+import jalview.xml.binding.jalview.Annotation.ThresholdLine;
+import jalview.xml.binding.jalview.AnnotationColourScheme;
+import jalview.xml.binding.jalview.AnnotationElement;
+import jalview.xml.binding.jalview.Feature;
+import jalview.xml.binding.jalview.Feature.OtherData;
+import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
+import jalview.xml.binding.jalview.FilterBy;
+import jalview.xml.binding.jalview.JalviewModel;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group;
+import jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting;
+import jalview.xml.binding.jalview.JalviewModel.JGroup;
+import jalview.xml.binding.jalview.JalviewModel.JSeq;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
+import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
+import jalview.xml.binding.jalview.JalviewModel.Tree;
+import jalview.xml.binding.jalview.JalviewModel.UserColours;
+import jalview.xml.binding.jalview.JalviewModel.Viewport;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.MapListType.MapListFrom;
+import jalview.xml.binding.jalview.MapListType.MapListTo;
+import jalview.xml.binding.jalview.Mapping;
+import jalview.xml.binding.jalview.NoValueColour;
+import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.Pdbentry.Property;
+import jalview.xml.binding.jalview.Sequence;
+import jalview.xml.binding.jalview.Sequence.DBRef;
+import jalview.xml.binding.jalview.SequenceSet;
+import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
+import jalview.xml.binding.jalview.ThresholdType;
+import jalview.xml.binding.jalview.VAMSAS;
import java.awt.Color;
+import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.DataInputStream;
@@ -124,12 +139,14 @@ import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Enumeration;
+import java.util.GregorianCalendar;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
@@ -147,9 +164,14 @@ import java.util.jar.JarOutputStream;
import javax.swing.JInternalFrame;
import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
/**
* Write out the current jalview desktop state as a Jalview XML stream.
@@ -204,6 +226,45 @@ public class Jalview2XML
private Map rnaSessions = new HashMap<>();
/**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the boolean value, or false
+ * if null.
+ *
+ * @param b
+ * @return
+ */
+ public static boolean safeBoolean(Boolean b)
+ {
+ return b == null ? false : b.booleanValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the integer value, or zero
+ * if null.
+ *
+ * @param i
+ * @return
+ */
+ public static int safeInt(Integer i)
+ {
+ return i == null ? 0 : i.intValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the float value, or zero if
+ * null.
+ *
+ * @param f
+ * @return
+ */
+ public static float safeFloat(Float f)
+ {
+ return f == null ? 0f : f.floatValue();
+ }
+
+ /**
* create/return unique hash string for sq
*
* @param sq
@@ -555,11 +616,12 @@ public class Jalview2XML
String shortName = makeFilename(af, shortNames);
- int ap, apSize = af.alignPanels.size();
+ int apSize = af.getAlignPanels().size();
- for (ap = 0; ap < apSize; ap++)
+ for (int ap = 0; ap < apSize; ap++)
{
- AlignmentPanel apanel = af.alignPanels.get(ap);
+ AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
+ .get(ap);
String fileName = apSize == 1 ? shortName : ap + shortName;
if (!fileName.endsWith(".xml"))
{
@@ -745,10 +807,21 @@ public class Jalview2XML
AlignViewport av = ap.av;
ViewportRanges vpRanges = av.getRanges();
- JalviewModel object = new JalviewModel();
- object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+ final ObjectFactory objectFactory = new ObjectFactory();
+ JalviewModel object = objectFactory.createJalviewModel();
+ object.setVamsasModel(new VAMSAS());
- object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ try
+ {
+ GregorianCalendar c = new GregorianCalendar();
+ DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
+ XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
+ object.setCreationDate(now);
+ } catch (DatatypeConfigurationException e)
+ {
+ System.err.println("error writing date: " + e.toString());
+ }
object.setVersion(
jalview.bin.Cache.getDefault("VERSION", "Development Build"));
@@ -765,7 +838,7 @@ public class Jalview2XML
SequenceSet vamsasSet = new SequenceSet();
Sequence vamsasSeq;
- JalviewModelSequence jms = new JalviewModelSequence();
+ // JalviewModelSequence jms = new JalviewModelSequence();
vamsasSet.setGapChar(jal.getGapCharacter() + "");
@@ -789,7 +862,8 @@ public class Jalview2XML
SequenceSetProperties ssp = new SequenceSetProperties();
ssp.setKey(key);
ssp.setValue(jal.getProperties().get(key).toString());
- vamsasSet.addSequenceSetProperties(ssp);
+ // vamsasSet.addSequenceSetProperties(ssp);
+ vamsasSet.getSequenceSetProperties().add(ssp);
}
}
@@ -826,7 +900,8 @@ public class Jalview2XML
else
{
vamsasSeq = createVamsasSequence(id, jds);
- vamsasSet.addSequence(vamsasSeq);
+// vamsasSet.addSequence(vamsasSeq);
+ vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
}
@@ -855,7 +930,8 @@ public class Jalview2XML
{
if (reps[h] != jds)
{
- jseq.addHiddenSequences(rjal.findIndex(reps[h]));
+ // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
+ jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
}
}
}
@@ -869,11 +945,11 @@ public class Jalview2XML
// TODO: omit sequence features from each alignment view's XML dump if we
// are storing dataset
- List sfs = jds
- .getSequenceFeatures();
+ List sfs = jds.getSequenceFeatures();
for (SequenceFeature sf : sfs)
{
- Features features = new Features();
+ // Features features = new Features();
+ Feature features = new Feature();
features.setBegin(sf.getBegin());
features.setEnd(sf.getEnd());
@@ -888,7 +964,8 @@ public class Jalview2XML
OtherData keyValue = new OtherData();
keyValue.setKey("LINK_" + l);
keyValue.setValue(sf.links.elementAt(l).toString());
- features.addOtherData(keyValue);
+ // features.addOtherData(keyValue);
+ features.getOtherData().add(keyValue);
}
}
if (sf.otherDetails != null)
@@ -910,7 +987,8 @@ public class Jalview2XML
otherData.setKey(key);
otherData.setKey2(subAttribute.getKey());
otherData.setValue(subAttribute.getValue().toString());
- features.addOtherData(otherData);
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
}
}
else
@@ -918,22 +996,23 @@ public class Jalview2XML
OtherData otherData = new OtherData();
otherData.setKey(key);
otherData.setValue(value.toString());
- features.addOtherData(otherData);
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
}
}
}
- jseq.addFeatures(features);
+ // jseq.addFeatures(features);
+ jseq.getFeatures().add(features);
}
if (jdatasq.getAllPDBEntries() != null)
{
- Enumeration en = jdatasq.getAllPDBEntries().elements();
+ Enumeration en = jdatasq.getAllPDBEntries().elements();
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
- .nextElement();
+ jalview.datamodel.PDBEntry entry = en.nextElement();
String pdbId = entry.getId();
pdb.setId(pdbId);
@@ -999,25 +1078,28 @@ public class Jalview2XML
Enumeration props = entry.getProperties();
if (props.hasMoreElements())
{
- PdbentryItem item = new PdbentryItem();
+ // PdbentryItem item = new PdbentryItem();
while (props.hasMoreElements())
{
Property prop = new Property();
String key = props.nextElement();
prop.setName(key);
prop.setValue(entry.getProperty(key).toString());
- item.addProperty(prop);
+ // item.addProperty(prop);
+ pdb.getProperty().add(prop);
}
- pdb.addPdbentryItem(item);
+ // pdb.addPdbentryItem(item);
}
- jseq.addPdbids(pdb);
+ // jseq.addPdbids(pdb);
+ jseq.getPdbids().add(pdb);
}
}
saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
- jms.addJSeq(jseq);
+ // jms.addJSeq(jseq);
+ object.getJSeq().add(jseq);
}
if (!storeDS && av.hasHiddenRows())
@@ -1044,12 +1126,14 @@ public class Jalview2XML
alcmap.setDnasq(seqHash(dnas[m]));
alcmap.setMapping(
createVamsasMapping(pmaps[m], dnas[m], null, false));
- alc.addAlcodMap(alcmap);
+ // alc.addAlcodMap(alcmap);
+ alc.getAlcodMap().add(alcmap);
hasMap = true;
}
if (hasMap)
{
- vamsasSet.addAlcodonFrame(alc);
+ // vamsasSet.addAlcodonFrame(alc);
+ vamsasSet.getAlcodonFrame().add(alc);
}
}
// TODO: delete this ? dead code from 2.8.3->2.9 ?
@@ -1102,13 +1186,13 @@ public class Jalview2XML
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.getAlignment() == jal)
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
{
- Tree tree = new Tree();
+ JalviewModel.Tree tree = new JalviewModel.Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.treeCanvas.threshold);
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
tree.setFitToWindow(tp.fitToWindow.getState());
tree.setFontName(tp.getTreeFont().getName());
@@ -1124,7 +1208,8 @@ public class Jalview2XML
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
tree.setId(makeHashCode(tp, null));
- jms.addTree(tree);
+ // jms.addTree(tree);
+ object.getTree().add(tree);
}
}
}
@@ -1188,7 +1273,8 @@ public class Jalview2XML
if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
jGroup.setColour(
- setUserColourScheme(colourScheme, userColours, jms));
+ setUserColourScheme(colourScheme, userColours,
+ object));
}
else
{
@@ -1200,12 +1286,12 @@ public class Jalview2XML
jGroup.setColour("AnnotationColourGradient");
jGroup.setAnnotationColours(constructAnnotationColours(
(jalview.schemes.AnnotationColourGradient) colourScheme,
- userColours, jms));
+ userColours, object));
}
else if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
jGroup.setColour(
- setUserColourScheme(colourScheme, userColours, jms));
+ setUserColourScheme(colourScheme, userColours, object));
}
else
{
@@ -1229,11 +1315,17 @@ public class Jalview2XML
jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
for (SequenceI seq : sg.getSequences())
{
- jGroup.addSeq(seqHash(seq));
+ // jGroup.addSeq(seqHash(seq));
+ jGroup.getSeq().add(seqHash(seq));
}
}
- jms.setJGroup(groups);
+ //jms.setJGroup(groups);
+ Object group;
+ for (JGroup grp : groups)
+ {
+ object.getJGroup().add(grp);
+ }
}
if (!storeDS)
{
@@ -1247,7 +1339,7 @@ public class Jalview2XML
{
view.setComplementId(av.getCodingComplement().getViewId());
}
- view.setViewName(av.viewName);
+ view.setViewName(av.getViewName());
view.setGatheredViews(av.isGatherViewsHere());
Rectangle size = ap.av.getExplodedGeometry();
@@ -1277,15 +1369,15 @@ public class Jalview2XML
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
+ userColours, object));
}
else if (av
.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
{
- AnnotationColours ac = constructAnnotationColours(
+ AnnotationColourScheme ac = constructAnnotationColours(
(jalview.schemes.AnnotationColourGradient) av
.getGlobalColourScheme(),
- userColours, jms);
+ userColours, object);
view.setAnnotationColours(ac);
view.setBgColour("AnnotationColourGradient");
@@ -1306,7 +1398,7 @@ public class Jalview2XML
view.setConsThreshold(vcs.getConservationInc());
if (cs instanceof jalview.schemes.UserColourScheme)
{
- view.setBgColour(setUserColourScheme(cs, userColours, jms));
+ view.setBgColour(setUserColourScheme(cs, userColours, object));
}
}
view.setPidThreshold(vcs.getThreshold());
@@ -1314,9 +1406,10 @@ public class Jalview2XML
view.setConservationSelected(av.getConservationSelected());
view.setPidSelected(av.getAbovePIDThreshold());
- view.setFontName(av.font.getName());
- view.setFontSize(av.font.getSize());
- view.setFontStyle(av.font.getStyle());
+ final Font font = av.getFont();
+ view.setFontName(font.getName());
+ view.setFontSize(font.getSize());
+ view.setFontStyle(font.getStyle());
view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
view.setRenderGaps(av.isRenderGaps());
view.setShowAnnotation(av.isShowAnnotation());
@@ -1343,7 +1436,7 @@ public class Jalview2XML
view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
if (av.getFeaturesDisplayed() != null)
{
- jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
+ FeatureSettings fs = new FeatureSettings();
FeatureRenderer fr = ap.getSeqPanel().seqCanvas
.getFeatureRenderer();
@@ -1354,7 +1447,7 @@ public class Jalview2XML
{
for (String featureType : renderOrder)
{
- Setting setting = new Setting();
+ FeatureSettings.Setting setting = new FeatureSettings.Setting();
setting.setType(featureType);
/*
@@ -1381,7 +1474,12 @@ public class Jalview2XML
setting.setColourByLabel(fcol.isColourByLabel());
if (fcol.isColourByAttribute())
{
- setting.setAttributeName(fcol.getAttributeName());
+ String[] attName = fcol.getAttributeName();
+ setting.getAttributeName().add(attName[0]);
+ if (attName.length > 1)
+ {
+ setting.getAttributeName().add(attName[1]);
+ }
}
setting.setAutoScale(fcol.isAutoScaled());
setting.setThreshold(fcol.getThreshold());
@@ -1415,7 +1513,8 @@ public class Jalview2XML
{
setting.setOrder(rorder);
}
- fs.addSetting(setting);
+ /// fs.addSetting(setting);
+ fs.getSetting().add(setting);
settingsAdded.addElement(featureType);
}
}
@@ -1434,10 +1533,12 @@ public class Jalview2XML
g.setName(grp);
g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
.booleanValue());
- fs.addGroup(g);
+ // fs.addGroup(g);
+ fs.getGroup().add(g);
groupsAdded.addElement(grp);
}
- jms.setFeatureSettings(fs);
+ // jms.setFeatureSettings(fs);
+ object.setFeatureSettings(fs);
}
if (av.hasHiddenColumns())
@@ -1457,7 +1558,8 @@ public class Jalview2XML
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ // view.addHiddenColumns(hc);
+ view.getHiddenColumns().add(hc);
}
}
}
@@ -1471,16 +1573,19 @@ public class Jalview2XML
// Some calcIds have no parameters.
if (cidp != null)
{
- view.addCalcIdParam(cidp);
+ // view.addCalcIdParam(cidp);
+ view.getCalcIdParam().add(cidp);
}
}
}
}
- jms.addViewport(view);
+ // jms.addViewport(view);
+ object.getViewport().add(view);
}
- object.setJalviewModelSequence(jms);
- object.getVamsasModel().addSequenceSet(vamsasSet);
+ // object.setJalviewModelSequence(jms);
+ // object.getVamsasModel().addSequenceSet(vamsasSet);
+ object.getVamsasModel().getSequenceSet().add(vamsasSet);
if (jout != null && fileName != null)
{
@@ -1494,13 +1599,23 @@ public class Jalview2XML
jout.putNextEntry(entry);
PrintWriter pout = new PrintWriter(
new OutputStreamWriter(jout, UTF_8));
- Marshaller marshaller = new Marshaller(pout);
- marshaller.marshal(object);
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewModel.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+
+ // output pretty printed
+ // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewModel(object), pout);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
pout.flush();
jout.closeEntry();
} catch (Exception ex)
{
// TODO: raise error in GUI if marshalling failed.
+ System.err.println("Error writing Jalview project");
ex.printStackTrace();
}
}
@@ -1561,7 +1676,8 @@ public class Jalview2XML
rna.setHeight(varna.getHeight());
rna.setDividerLocation(varna.getDividerLocation());
rna.setSelectedRna(varna.getSelectedIndex());
- jseq.addRnaViewer(rna);
+ // jseq.addRnaViewer(rna);
+ jseq.getRnaViewer().add(rna);
/*
* Store each Varna panel's state once in the project per sequence.
@@ -1597,7 +1713,8 @@ public class Jalview2XML
ss.setViewerState(jarEntryName);
ss.setGapped(model.gapped);
ss.setTitle(model.title);
- rna.addSecondaryStructure(ss);
+ // rna.addSecondaryStructure(ss);
+ rna.getSecondaryStructure().add(ss);
}
}
}
@@ -1736,7 +1853,8 @@ public class Jalview2XML
state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
state.setColourByJmol(viewFrame.isColouredByViewer());
state.setType(viewFrame.getViewerType().toString());
- pdb.addStructureState(state);
+ // pdb.addStructureState(state);
+ pdb.getStructureState().add(state);
}
}
}
@@ -1744,19 +1862,19 @@ public class Jalview2XML
}
/**
- * Populates the AnnotationColours xml for save. This captures the settings of
- * the options in the 'Colour by Annotation' dialog.
+ * Populates the AnnotationColourScheme xml for save. This captures the
+ * settings of the options in the 'Colour by Annotation' dialog.
*
* @param acg
* @param userColours
- * @param jms
+ * @param jm
* @return
*/
- private AnnotationColours constructAnnotationColours(
+ private AnnotationColourScheme constructAnnotationColours(
AnnotationColourGradient acg, List userColours,
- JalviewModelSequence jms)
+ JalviewModel jm)
{
- AnnotationColours ac = new AnnotationColours();
+ AnnotationColourScheme ac = new AnnotationColourScheme();
ac.setAboveThreshold(acg.getAboveThreshold());
ac.setThreshold(acg.getAnnotationThreshold());
// 2.10.2 save annotationId (unique) not annotation label
@@ -1764,7 +1882,7 @@ public class Jalview2XML
if (acg.getBaseColour() instanceof UserColourScheme)
{
ac.setColourScheme(
- setUserColourScheme(acg.getBaseColour(), userColours, jms));
+ setUserColourScheme(acg.getBaseColour(), userColours, jm));
}
else
{
@@ -1870,10 +1988,11 @@ public class Jalview2XML
{
for (String pr : annotation.getProperties())
{
- Property prop = new Property();
+ jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
prop.setName(pr);
prop.setValue(annotation.getProperty(pr));
- an.addProperty(prop);
+ // an.addProperty(prop);
+ an.getProperty().add(prop);
}
}
@@ -1917,7 +2036,8 @@ public class Jalview2XML
ae.setColour(annotation.annotations[a].colour.getRGB());
}
- an.addAnnotationElement(ae);
+ // an.addAnnotationElement(ae);
+ an.getAnnotationElement().add(ae);
if (annotation.autoCalculated)
{
// only write one non-null entry into the annotation row -
@@ -1935,7 +2055,8 @@ public class Jalview2XML
{
// skip autocalculated annotation - these are only provided for
// alignments
- vamsasSet.addAnnotation(an);
+ // vamsasSet.addAnnotation(an);
+ vamsasSet.getAnnotation().add(an);
}
}
@@ -1948,12 +2069,14 @@ public class Jalview2XML
{
CalcIdParam vCalcIdParam = new CalcIdParam();
vCalcIdParam.setCalcId(calcId);
- vCalcIdParam.addServiceURL(settings.getServiceURI());
+ // vCalcIdParam.addServiceURL(settings.getServiceURI());
+ vCalcIdParam.getServiceURL().add(settings.getServiceURI());
// generic URI allowing a third party to resolve another instance of the
// service used for this calculation
- for (String urls : settings.getServiceURLs())
+ for (String url : settings.getServiceURLs())
{
- vCalcIdParam.addServiceURL(urls);
+ // vCalcIdParam.addServiceURL(urls);
+ vCalcIdParam.getServiceURL().add(url);
}
vCalcIdParam.setVersion("1.0");
if (settings.getPreset() != null)
@@ -1985,8 +2108,9 @@ public class Jalview2XML
{
if (calcIdParam.getVersion().equals("1.0"))
{
+ final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
Jws2Instance service = Jws2Discoverer.getDiscoverer()
- .getPreferredServiceFor(calcIdParam.getServiceURL());
+ .getPreferredServiceFor(calcIds);
if (service != null)
{
WsParamSetI parmSet = null;
@@ -1994,7 +2118,7 @@ public class Jalview2XML
{
parmSet = service.getParamStore().parseServiceParameterFile(
calcIdParam.getName(), calcIdParam.getDescription(),
- calcIdParam.getServiceURL(),
+ calcIds,
calcIdParam.getParameters().replace("|\\n|", "\n"));
} catch (IOException x)
{
@@ -2140,7 +2264,8 @@ public class Jalview2XML
jds, recurse);
dbref.setMapping(mp);
}
- vamsasSeq.addDBRef(dbref);
+ // vamsasSeq.addDBRef(dbref);
+ vamsasSeq.getDBRef().add(dbref);
}
}
return vamsasSeq;
@@ -2161,7 +2286,8 @@ public class Jalview2XML
MapListFrom mfrom = new MapListFrom();
mfrom.setStart(range[0]);
mfrom.setEnd(range[1]);
- mp.addMapListFrom(mfrom);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
}
r = mlst.getToRanges();
for (int[] range : r)
@@ -2169,13 +2295,14 @@ public class Jalview2XML
MapListTo mto = new MapListTo();
mto.setStart(range[0]);
mto.setEnd(range[1]);
- mp.addMapListTo(mto);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
}
- mp.setMapFromUnit(mlst.getFromRatio());
- mp.setMapToUnit(mlst.getToRatio());
+ mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
if (jmp.getTo() != null)
{
- MappingChoice mpc = new MappingChoice();
+ // MappingChoice mpc = new MappingChoice();
// check/create ID for the sequence referenced by getTo()
@@ -2191,25 +2318,26 @@ public class Jalview2XML
{
jmpid = seqHash(ps = parentseq);
}
- mpc.setDseqFor(jmpid);
- if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ // mpc.setDseqFor(jmpid);
+ mp.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(jmpid))
{
jalview.bin.Cache.log.debug("creatign new DseqFor ID");
- seqRefIds.put(mpc.getDseqFor(), ps);
+ seqRefIds.put(jmpid, ps);
}
else
{
jalview.bin.Cache.log.debug("reusing DseqFor ID");
}
- mp.setMappingChoice(mpc);
+ // mp.setMappingChoice(mpc);
}
}
return mp;
}
String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
- List userColours, JalviewModelSequence jms)
+ List userColours, JalviewModel jm)
{
String id = null;
jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
@@ -2224,48 +2352,60 @@ public class Jalview2XML
{
// actually create the scheme's entry in the XML model
java.awt.Color[] colours = ucs.getColours();
- jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
- jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+ UserColours uc = new UserColours();
+ // UserColourScheme jbucs = new UserColourScheme();
+ JalviewUserColours jbucs = new JalviewUserColours();
for (int i = 0; i < colours.length; i++)
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ Colour col = new Colour();
col.setName(ResidueProperties.aa[i]);
col.setRGB(jalview.util.Format.getHexString(colours[i]));
- jbucs.addColour(col);
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
}
if (ucs.getLowerCaseColours() != null)
{
colours = ucs.getLowerCaseColours();
for (int i = 0; i < colours.length; i++)
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ Colour col = new Colour();
col.setName(ResidueProperties.aa[i].toLowerCase());
col.setRGB(jalview.util.Format.getHexString(colours[i]));
- jbucs.addColour(col);
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
}
}
uc.setId(id);
uc.setUserColourScheme(jbucs);
- jms.addUserColours(uc);
+ // jm.addUserColours(uc);
+ jm.getUserColours().add(uc);
}
return id;
}
jalview.schemes.UserColourScheme getUserColourScheme(
- JalviewModelSequence jms, String id)
+ JalviewModel jm, String id)
{
- UserColours[] uc = jms.getUserColours();
+ List uc = jm.getUserColours();
UserColours colours = null;
-
+/*
for (int i = 0; i < uc.length; i++)
{
if (uc[i].getId().equals(id))
{
colours = uc[i];
-
+ break;
+ }
+ }
+*/
+ for (UserColours c : uc)
+ {
+ if (c.getId().equals(id))
+ {
+ colours = c;
break;
}
}
@@ -2275,19 +2415,22 @@ public class Jalview2XML
for (int i = 0; i < 24; i++)
{
newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ // colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ colours.getUserColourScheme().getColour().get(i).getRGB(),
+ 16));
}
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
newColours);
- if (colours.getUserColourScheme().getColourCount() > 24)
+ if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
{
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i + 24).getRGB(),
+ colours.getUserColourScheme().getColour().get(i + 24)
+ .getRGB(),
16));
}
ucs.setLowerCaseColours(newColours);
@@ -2305,7 +2448,7 @@ public class Jalview2XML
* flag to control whether the Jalview2XML_V1 parser should be deferred to if
* exceptions are raised during project XML parsing
*/
- public boolean attemptversion1parse = true;
+ public boolean attemptversion1parse = false;
/**
* Load a jalview project archive from a jar file
@@ -2329,8 +2472,10 @@ public class Jalview2XML
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = loadJalviewAlign(jprovider);
- af.setMenusForViewport();
-
+ if (af != null)
+ {
+ af.setMenusForViewport();
+ }
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
@@ -2435,32 +2580,45 @@ public class Jalview2XML
if (jarentry != null && jarentry.getName().endsWith(".xml"))
{
InputStreamReader in = new InputStreamReader(jin, UTF_8);
- JalviewModel object = new JalviewModel();
+ // JalviewModel object = new JalviewModel();
+
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(jin);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ JAXBElement jbe = um
+ .unmarshal(streamReader, JalviewModel.class);
+ JalviewModel object = jbe.getValue();
+ /*
Unmarshaller unmar = new Unmarshaller(object);
unmar.setValidation(false);
object = (JalviewModel) unmar.unmarshal(in);
+ */
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
- if (_af != null && object.getJalviewModelSequence()
- .getViewportCount() > 0)
+ if (_af != null && object.getViewport().size() > 0)
+ // getJalviewModelSequence().getViewportCount() > 0)
{
if (af == null)
{
// store a reference to the first view
af = _af;
}
- if (_af.viewport.isGatherViewsHere())
+ if (_af.getViewport().isGatherViewsHere())
{
// if this is a gathered view, keep its reference since
// after gathering views, only this frame will remain
af = _af;
- gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
+ gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
+ _af);
}
// Save dataset to register mappings once all resolved
- importedDatasets.put(af.viewport.getAlignment().getDataset(),
- af.viewport.getAlignment().getDataset());
+ importedDatasets.put(
+ af.getViewport().getAlignment().getDataset(),
+ af.getViewport().getAlignment().getDataset());
}
}
entryCount++;
@@ -2484,16 +2642,7 @@ public class Jalview2XML
ex.printStackTrace(System.err);
if (attemptversion1parse)
{
- // Is Version 1 Jar file?
- try
- {
- af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
- } catch (Exception ex2)
- {
- System.err.println("Exception whilst loading as jalviewXMLV1:");
- ex2.printStackTrace();
- af = null;
- }
+ // used to attempt to parse as V1 castor-generated xml
}
if (Desktop.instance != null)
{
@@ -2594,7 +2743,7 @@ public class Jalview2XML
addedToSplitFrames.add(af);
dnaFrame.setMenusForViewport();
af.setMenusForViewport();
- if (af.viewport.isGatherViewsHere())
+ if (af.getViewport().isGatherViewsHere())
{
gatherTo.add(sf);
}
@@ -2613,8 +2762,8 @@ public class Jalview2XML
if (!addedToSplitFrames.contains(af))
{
Viewport view = candidate.getKey();
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
- view.getHeight());
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
af.setMenusForViewport();
System.err.println("Failed to restore view " + view.getTitle()
+ " to split frame");
@@ -2658,7 +2807,7 @@ public class Jalview2XML
* And compute cDNA consensus (couldn't do earlier with consensus as
* mappings were not yet present)
*/
- proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+ proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
return splitFrame;
}
@@ -2846,7 +2995,7 @@ public class Jalview2XML
/**
* Load alignment frame from jalview XML DOM object
*
- * @param object
+ * @param jalviewModel
* DOM
* @param file
* filename source string
@@ -2856,15 +3005,18 @@ public class Jalview2XML
* data source provider
* @return alignment frame created from view stored in DOM
*/
- AlignFrame loadFromObject(JalviewModel object, String file,
+ AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
- Sequence[] vamsasSeq = vamsasSet.getSequence();
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ List vamsasSeqs = vamsasSet.getSequence();
- JalviewModelSequence jms = object.getJalviewModelSequence();
+ // JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ // : null;
+ Viewport view = (jalviewModel.getViewport().size() > 0)
+ ? jalviewModel.getViewport().get(0)
: null;
// ////////////////////////////////
@@ -2876,11 +3028,13 @@ public class Jalview2XML
boolean multipleView = false;
SequenceI referenceseqForView = null;
- JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
+ // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
+ List jseqs = jalviewModel.getJSeq();
int vi = 0; // counter in vamsasSeq array
- for (int i = 0; i < jseqs.length; i++)
+ for (int i = 0; i < jseqs.size(); i++)
{
- String seqId = jseqs[i].getId();
+ JSeq jseq = jseqs.get(i);
+ String seqId = jseq.getId();
SequenceI tmpSeq = seqRefIds.get(seqId);
if (tmpSeq != null)
@@ -2888,25 +3042,26 @@ public class Jalview2XML
if (!incompleteSeqs.containsKey(seqId))
{
// may not need this check, but keep it for at least 2.9,1 release
- if (tmpSeq.getStart() != jseqs[i].getStart()
- || tmpSeq.getEnd() != jseqs[i].getEnd())
+ if (tmpSeq.getStart() != jseq.getStart()
+ || tmpSeq.getEnd() != jseq.getEnd())
{
System.err.println(
"Warning JAL-2154 regression: updating start/end for sequence "
- + tmpSeq.toString() + " to " + jseqs[i]);
+ + tmpSeq.toString() + " to " + jseq);
}
}
else
{
incompleteSeqs.remove(seqId);
}
- if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
+ if (vamsasSeqs.size() > vi
+ && vamsasSeqs.get(vi).getId().equals(seqId))
{
// most likely we are reading a dataset XML document so
// update from vamsasSeq section of XML for this sequence
- tmpSeq.setName(vamsasSeq[vi].getName());
- tmpSeq.setDescription(vamsasSeq[vi].getDescription());
- tmpSeq.setSequence(vamsasSeq[vi].getSequence());
+ tmpSeq.setName(vamsasSeqs.get(vi).getName());
+ tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
+ tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
vi++;
}
else
@@ -2914,29 +3069,30 @@ public class Jalview2XML
// reading multiple views, so vamsasSeq set is a subset of JSeq
multipleView = true;
}
- tmpSeq.setStart(jseqs[i].getStart());
- tmpSeq.setEnd(jseqs[i].getEnd());
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
tmpseqs.add(tmpSeq);
}
else
{
- tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
- vamsasSeq[vi].getSequence());
- tmpSeq.setDescription(vamsasSeq[vi].getDescription());
- tmpSeq.setStart(jseqs[i].getStart());
- tmpSeq.setEnd(jseqs[i].getEnd());
+ Sequence vamsasSeq = vamsasSeqs.get(vi);
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
+ vamsasSeq.getSequence());
+ tmpSeq.setDescription(vamsasSeq.getDescription());
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+ seqRefIds.put(vamsasSeq.getId(), tmpSeq);
tmpseqs.add(tmpSeq);
vi++;
}
- if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+ if (safeBoolean(jseq.isViewreference()))
{
referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
}
- if (jseqs[i].getHidden())
+ if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
{
if (hiddenSeqs == null)
{
@@ -2965,8 +3121,7 @@ public class Jalview2XML
}
else
{
- boolean isdsal = object.getJalviewModelSequence()
- .getViewportCount() == 0;
+ boolean isdsal = jalviewModel.getViewport().isEmpty();
if (isdsal)
{
// we are importing a dataset record, so
@@ -2993,9 +3148,10 @@ public class Jalview2XML
al.setSeqrep(referenceseqForView);
}
// / Add the alignment properties
- for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
{
- SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
+ .get(i);
al.setProperty(ssp.getKey(), ssp.getValue());
}
@@ -3012,26 +3168,27 @@ public class Jalview2XML
// now, for 2.10 projects, this is also done if the xml doc includes
// dataset sequences not actually present in any particular view.
//
- for (int i = 0; i < vamsasSeq.length; i++)
+ for (int i = 0; i < vamsasSeqs.size(); i++)
{
- if (jseqs[i].getFeaturesCount() > 0)
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getFeatures().size() > 0)
{
- Features[] features = jseqs[i].getFeatures();
- for (int f = 0; f < features.length; f++)
+ List features = jseq.getFeatures();
+ for (int f = 0; f < features.size(); f++)
{
- SequenceFeature sf = new SequenceFeature(features[f].getType(),
- features[f].getDescription(), features[f].getBegin(),
- features[f].getEnd(), features[f].getScore(),
- features[f].getFeatureGroup());
- sf.setStatus(features[f].getStatus());
+ Feature feat = features.get(f);
+ SequenceFeature sf = new SequenceFeature(feat.getType(),
+ feat.getDescription(), feat.getBegin(), feat.getEnd(),
+ safeFloat(feat.getScore()), feat.getFeatureGroup());
+ sf.setStatus(feat.getStatus());
/*
* load any feature attributes - include map-valued attributes
*/
Map> mapAttributes = new HashMap<>();
- for (int od = 0; od < features[f].getOtherDataCount(); od++)
+ for (int od = 0; od < feat.getOtherData().size(); od++)
{
- OtherData keyValue = features[f].getOtherData(od);
+ OtherData keyValue = feat.getOtherData().get(od);
String attributeName = keyValue.getKey();
String attributeValue = keyValue.getValue();
if (attributeName.startsWith("LINK"))
@@ -3068,27 +3225,28 @@ public class Jalview2XML
al.getSequenceAt(i).addSequenceFeature(sf);
}
}
- if (vamsasSeq[i].getDBRefCount() > 0)
+ if (vamsasSeqs.get(i).getDBRef().size() > 0)
{
// adds dbrefs to datasequence's set (since Jalview 2.10)
addDBRefs(
al.getSequenceAt(i).getDatasetSequence() == null
? al.getSequenceAt(i)
: al.getSequenceAt(i).getDatasetSequence(),
- vamsasSeq[i]);
+ vamsasSeqs.get(i));
}
- if (jseqs[i].getPdbidsCount() > 0)
+ if (jseq.getPdbids().size() > 0)
{
- Pdbids[] ids = jseqs[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ List ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
{
+ Pdbids pdbid = ids.get(p);
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(ids[p].getId());
- if (ids[p].getType() != null)
+ entry.setId(pdbid.getId());
+ if (pdbid.getType() != null)
{
- if (PDBEntry.Type.getType(ids[p].getType()) != null)
+ if (PDBEntry.Type.getType(pdbid.getType()) != null)
{
- entry.setType(PDBEntry.Type.getType(ids[p].getType()));
+ entry.setType(PDBEntry.Type.getType(pdbid.getType()));
}
else
{
@@ -3096,21 +3254,22 @@ public class Jalview2XML
}
}
// jprovider is null when executing 'New View'
- if (ids[p].getFile() != null && jprovider != null)
+ if (pdbid.getFile() != null && jprovider != null)
{
- if (!pdbloaded.containsKey(ids[p].getFile()))
+ if (!pdbloaded.containsKey(pdbid.getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
- ids[p].getFile()));
+ entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile()));
}
else
{
- entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+ entry.setFile(pdbloaded.get(pdbid.getId()).toString());
}
}
- if (ids[p].getPdbentryItem() != null)
+ /*
+ if (pdbid.getPdbentryItem() != null)
{
- for (PdbentryItem item : ids[p].getPdbentryItem())
+ for (PdbentryItem item : pdbid.getPdbentryItem())
{
for (Property pr : item.getProperty())
{
@@ -3118,6 +3277,11 @@ public class Jalview2XML
}
}
}
+ */
+ for (Property prop : pdbid.getProperty())
+ {
+ entry.setProperty(prop.getName(), prop.getValue());
+ }
StructureSelectionManager
.getStructureSelectionManager(Desktop.instance)
.registerPDBEntry(entry);
@@ -3138,26 +3302,27 @@ public class Jalview2XML
// ///////////////////////////////
// LOAD SEQUENCE MAPPINGS
- if (vamsasSet.getAlcodonFrameCount() > 0)
+ if (vamsasSet.getAlcodonFrame().size() > 0)
{
// TODO Potentially this should only be done once for all views of an
// alignment
- AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
- for (int i = 0; i < alc.length; i++)
+ List alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.size(); i++)
{
AlignedCodonFrame cf = new AlignedCodonFrame();
- if (alc[i].getAlcodMapCount() > 0)
+ if (alc.get(i).getAlcodMap().size() > 0)
{
- AlcodMap[] maps = alc[i].getAlcodMap();
- for (int m = 0; m < maps.length; m++)
+ List maps = alc.get(i).getAlcodMap();
+ for (int m = 0; m < maps.size(); m++)
{
- SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
+ AlcodMap map = maps.get(m);
+ SequenceI dnaseq = seqRefIds.get(map.getDnasq());
// Load Mapping
jalview.datamodel.Mapping mapping = null;
// attach to dna sequence reference.
- if (maps[m].getMapping() != null)
+ if (map.getMapping() != null)
{
- mapping = addMapping(maps[m].getMapping());
+ mapping = addMapping(map.getMapping());
if (dnaseq != null && mapping.getTo() != null)
{
cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
@@ -3166,7 +3331,7 @@ public class Jalview2XML
{
// defer to later
frefedSequence.add(
- newAlcodMapRef(maps[m].getDnasq(), cf, mapping));
+ newAlcodMapRef(map.getDnasq(), cf, mapping));
}
}
}
@@ -3184,13 +3349,13 @@ public class Jalview2XML
*/
Map> groupAnnotRefs = new Hashtable<>();
- if (vamsasSet.getAnnotationCount() > 0)
+ if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
{
- Annotation[] an = vamsasSet.getAnnotation();
+ List an = vamsasSet.getAnnotation();
- for (int i = 0; i < an.length; i++)
+ for (int i = 0; i < an.size(); i++)
{
- Annotation annotation = an[i];
+ Annotation annotation = an.get(i);
/**
* test if annotation is automatically calculated for this view only
@@ -3202,29 +3367,29 @@ public class Jalview2XML
{
// Kludge for pre 2.5 projects which lacked the autocalculated flag
autoForView = true;
- if (!annotation.hasAutoCalculated())
- {
- annotation.setAutoCalculated(true);
- }
+ // JAXB has no has() test; schema defaults value to false
+ // if (!annotation.hasAutoCalculated())
+ // {
+ // annotation.setAutoCalculated(true);
+ // }
}
- if (autoForView || (annotation.hasAutoCalculated()
- && annotation.isAutoCalculated()))
+ if (autoForView || annotation.isAutoCalculated())
{
// remove ID - we don't recover annotation from other views for
// view-specific annotation
annotation.setId(null);
}
- // set visiblity for other annotation in this view
+ // set visibility for other annotation in this view
String annotationId = annotation.getId();
if (annotationId != null && annotationIds.containsKey(annotationId))
{
AlignmentAnnotation jda = annotationIds.get(annotationId);
// in principle Visible should always be true for annotation displayed
// in multiple views
- if (annotation.hasVisible())
+ if (annotation.isVisible() != null)
{
- jda.visible = annotation.getVisible();
+ jda.visible = annotation.isVisible();
}
al.addAnnotation(jda);
@@ -3232,41 +3397,36 @@ public class Jalview2XML
continue;
}
// Construct new annotation from model.
- AnnotationElement[] ae = annotation.getAnnotationElement();
+ List ae = annotation.getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
java.awt.Color firstColour = null;
int anpos;
- if (!annotation.getScoreOnly())
+ if (!annotation.isScoreOnly())
{
anot = new jalview.datamodel.Annotation[al.getWidth()];
- for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
{
- anpos = ae[aa].getPosition();
+ AnnotationElement annElement = ae.get(aa);
+ anpos = annElement.getPosition();
if (anpos >= anot.length)
{
continue;
}
+ float value = safeFloat(annElement.getValue());
anot[anpos] = new jalview.datamodel.Annotation(
-
- ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
- (ae[aa].getSecondaryStructure() == null
- || ae[aa].getSecondaryStructure().length() == 0)
- ? ' '
- : ae[aa].getSecondaryStructure()
- .charAt(0),
- ae[aa].getValue()
-
- );
- // JBPNote: Consider verifying dataflow for IO of secondary
- // structure annotation read from Stockholm files
- // this was added to try to ensure that
- // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
- // {
- // anot[ae[aa].getPosition()].displayCharacter = "";
- // }
- anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ annElement.getDisplayCharacter(),
+ annElement.getDescription(),
+ (annElement.getSecondaryStructure() == null
+ || annElement.getSecondaryStructure()
+ .length() == 0)
+ ? ' '
+ : annElement
+ .getSecondaryStructure()
+ .charAt(0),
+ value);
+ anot[anpos].colour = new Color(safeInt(annElement.getColour()));
if (firstColour == null)
{
firstColour = anot[anpos].colour;
@@ -3275,7 +3435,7 @@ public class Jalview2XML
}
jalview.datamodel.AlignmentAnnotation jaa = null;
- if (annotation.getGraph())
+ if (annotation.isGraph())
{
float llim = 0, hlim = 0;
// if (autoForView || an[i].isAutoCalculated()) {
@@ -3283,18 +3443,17 @@ public class Jalview2XML
// }
jaa = new jalview.datamodel.AlignmentAnnotation(
annotation.getLabel(), annotation.getDescription(), anot,
- llim, hlim, annotation.getGraphType());
+ llim, hlim, safeInt(annotation.getGraphType()));
- jaa.graphGroup = annotation.getGraphGroup();
+ jaa.graphGroup = safeInt(annotation.getGraphGroup());
jaa._linecolour = firstColour;
if (annotation.getThresholdLine() != null)
{
jaa.setThreshold(new jalview.datamodel.GraphLine(
- annotation.getThresholdLine().getValue(),
+ safeFloat(annotation.getThresholdLine().getValue()),
annotation.getThresholdLine().getLabel(),
- new java.awt.Color(
- annotation.getThresholdLine().getColour())));
-
+ new java.awt.Color(safeInt(
+ annotation.getThresholdLine().getColour()))));
}
if (autoForView || annotation.isAutoCalculated())
{
@@ -3305,18 +3464,18 @@ public class Jalview2XML
}
else
{
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot);
jaa._linecolour = firstColour;
}
// register new annotation
- if (an[i].getId() != null)
+ if (annotation.getId() != null)
{
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
+ annotationIds.put(annotation.getId(), jaa);
+ jaa.annotationId = annotation.getId();
}
// recover sequence association
- String sequenceRef = an[i].getSequenceRef();
+ String sequenceRef = annotation.getSequenceRef();
if (sequenceRef != null)
{
// from 2.9 sequenceRef is to sequence id (JAL-1781)
@@ -3333,55 +3492,54 @@ public class Jalview2XML
}
}
// and make a note of any group association
- if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
+ if (annotation.getGroupRef() != null
+ && annotation.getGroupRef().length() > 0)
{
List aal = groupAnnotRefs
- .get(an[i].getGroupRef());
+ .get(annotation.getGroupRef());
if (aal == null)
{
aal = new ArrayList<>();
- groupAnnotRefs.put(an[i].getGroupRef(), aal);
+ groupAnnotRefs.put(annotation.getGroupRef(), aal);
}
aal.add(jaa);
}
- if (an[i].hasScore())
+ if (annotation.getScore() != null)
{
- jaa.setScore(an[i].getScore());
+ jaa.setScore(annotation.getScore().doubleValue());
}
- if (an[i].hasVisible())
+ if (annotation.isVisible() != null)
{
- jaa.visible = an[i].getVisible();
+ jaa.visible = annotation.isVisible().booleanValue();
}
- if (an[i].hasCentreColLabels())
+ if (annotation.isCentreColLabels() != null)
{
- jaa.centreColLabels = an[i].getCentreColLabels();
+ jaa.centreColLabels = annotation.isCentreColLabels()
+ .booleanValue();
}
- if (an[i].hasScaleColLabels())
+ if (annotation.isScaleColLabels() != null)
{
- jaa.scaleColLabel = an[i].getScaleColLabels();
+ jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
}
- if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
+ if (annotation.isAutoCalculated())
{
// 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.
}
- if (an[i].hasGraphHeight())
- {
- jaa.graphHeight = an[i].getGraphHeight();
- }
- if (an[i].hasBelowAlignment())
+ if (annotation.getGraphHeight() != null)
{
- jaa.belowAlignment = an[i].isBelowAlignment();
+ jaa.graphHeight = annotation.getGraphHeight().intValue();
}
- jaa.setCalcId(an[i].getCalcId());
- if (an[i].getPropertyCount() > 0)
+ jaa.belowAlignment = annotation.isBelowAlignment();
+ jaa.setCalcId(annotation.getCalcId());
+ if (annotation.getProperty().size() > 0)
{
- for (jalview.schemabinding.version2.Property prop : an[i]
+ for (Annotation.Property prop : annotation
.getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
@@ -3403,19 +3561,19 @@ public class Jalview2XML
// ///////////////////////
// LOAD GROUPS
// Create alignment markup and styles for this view
- if (jms.getJGroupCount() > 0)
+ if (jalviewModel.getJGroup().size() > 0)
{
- JGroup[] groups = jms.getJGroup();
+ List groups = jalviewModel.getJGroup();
boolean addAnnotSchemeGroup = false;
- for (int i = 0; i < groups.length; i++)
+ for (int i = 0; i < groups.size(); i++)
{
- JGroup jGroup = groups[i];
+ JGroup jGroup = groups.get(i);
ColourSchemeI cs = null;
if (jGroup.getColour() != null)
{
if (jGroup.getColour().startsWith("ucs"))
{
- cs = getUserColourScheme(jms, jGroup.getColour());
+ cs = getUserColourScheme(jalviewModel, jGroup.getColour());
}
else if (jGroup.getColour().equals("AnnotationColourGradient")
&& jGroup.getAnnotationColours() != null)
@@ -3428,13 +3586,13 @@ public class Jalview2XML
jGroup.getColour());
}
}
- int pidThreshold = jGroup.getPidThreshold();
+ int pidThreshold = safeInt(jGroup.getPidThreshold());
Vector seqs = new Vector<>();
- for (int s = 0; s < jGroup.getSeqCount(); s++)
+ for (int s = 0; s < jGroup.getSeq().size(); s++)
{
- String seqId = jGroup.getSeq(s) + "";
+ String seqId = jGroup.getSeq().get(s);
SequenceI ts = seqRefIds.get(seqId);
if (ts != null)
@@ -3449,37 +3607,26 @@ public class Jalview2XML
}
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
- jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
- jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
+ safeBoolean(jGroup.isDisplayBoxes()),
+ safeBoolean(jGroup.isDisplayText()),
+ safeBoolean(jGroup.isColourText()),
+ safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
sg.getGroupColourScheme().setThreshold(pidThreshold, true);
sg.getGroupColourScheme()
- .setConservationInc(jGroup.getConsThreshold());
- sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
-
- sg.textColour = new java.awt.Color(jGroup.getTextCol1());
- sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
- sg.setShowNonconserved(
- jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved()
- : false);
- sg.thresholdTextColour = jGroup.getTextColThreshold();
- if (jGroup.hasShowConsensusHistogram())
- {
+ .setConservationInc(safeInt(jGroup.getConsThreshold()));
+ sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
+
+ sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
+ sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
+ sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
+ sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
+ // attributes with a default in the schema are never null
sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- }
- ;
- if (jGroup.hasShowSequenceLogo())
- {
sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- }
- if (jGroup.hasNormaliseSequenceLogo())
- {
sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
- }
- if (jGroup.hasIgnoreGapsinConsensus())
- {
- sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus());
- }
- if (jGroup.getConsThreshold() != 0)
+ sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
+ if (jGroup.getConsThreshold() != null
+ && jGroup.getConsThreshold().intValue() != 0)
{
Conservation c = new Conservation("All", sg.getSequences(null), 0,
sg.getWidth() - 1);
@@ -3521,7 +3668,7 @@ public class Jalview2XML
{
// reconstruct the annotation colourscheme
sg.setColourScheme(constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jms, false));
+ jGroup.getAnnotationColours(), null, al, jalviewModel, false));
}
}
}
@@ -3578,7 +3725,7 @@ public class Jalview2XML
* Jalview 2.8.1 behaviour)
*/
boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
- object.getVersion());
+ jalviewModel.getVersion());
AlignmentPanel ap = null;
boolean isnewview = true;
@@ -3607,9 +3754,9 @@ public class Jalview2XML
if (isnewview)
{
- af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
+ af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
uniqueSeqSetId, viewId, autoAlan);
- av = af.viewport;
+ av = af.getViewport();
ap = af.alignPanel;
}
@@ -3620,7 +3767,7 @@ public class Jalview2XML
*/
if (loadTreesAndStructures)
{
- loadTrees(jms, view, af, av, ap);
+ loadTrees(jalviewModel, view, af, av, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
@@ -3642,7 +3789,7 @@ public class Jalview2XML
* @param ap
*/
private void loadRnaViewers(jarInputStreamProvider jprovider,
- JSeq[] jseqs, AlignmentPanel ap)
+ List jseqs, AlignmentPanel ap)
{
/*
* scan the sequences for references to viewers; create each one the first
@@ -3650,15 +3797,15 @@ public class Jalview2XML
*/
for (JSeq jseq : jseqs)
{
- for (int i = 0; i < jseq.getRnaViewerCount(); i++)
+ for (int i = 0; i < jseq.getRnaViewer().size(); i++)
{
- RnaViewer viewer = jseq.getRnaViewer(i);
+ RnaViewer viewer = jseq.getRnaViewer().get(i);
AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
ap);
- for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
+ for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
{
- SecondaryStructure ss = viewer.getSecondaryStructure(j);
+ SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
SequenceI seq = seqRefIds.get(jseq.getId());
AlignmentAnnotation ann = this.annotationIds
.get(ss.getAnnotationId());
@@ -3667,7 +3814,7 @@ public class Jalview2XML
* add the structure to the Varna display (with session state copied
* from the jar to a temporary file)
*/
- boolean gapped = ss.isGapped();
+ boolean gapped = safeBoolean(ss.isGapped());
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
@@ -3675,7 +3822,7 @@ public class Jalview2XML
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
- appVarna.setInitialSelection(viewer.getSelectedRna());
+ appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
}
}
}
@@ -3716,8 +3863,9 @@ public class Jalview2XML
* viewer not found - make it
*/
RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
- viewer.getXpos(), viewer.getYpos(), viewer.getWidth(),
- viewer.getHeight(), viewer.getDividerLocation());
+ safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
+ safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
+ safeInt(viewer.getDividerLocation()));
AppVarna varna = new AppVarna(model, ap);
return varna;
@@ -3726,30 +3874,30 @@ public class Jalview2XML
/**
* Load any saved trees
*
- * @param jms
+ * @param jm
* @param view
* @param af
* @param av
* @param ap
*/
- protected void loadTrees(JalviewModelSequence jms, Viewport view,
+ protected void loadTrees(JalviewModel jm, Viewport view,
AlignFrame af, AlignViewport av, AlignmentPanel ap)
{
// TODO result of automated refactoring - are all these parameters needed?
try
{
- for (int t = 0; t < jms.getTreeCount(); t++)
+ for (int t = 0; t < jm.getTree().size(); t++)
{
- Tree tree = jms.getTree(t);
+ Tree tree = jm.getTree().get(t);
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
- tp = af.showNewickTree(
- new jalview.io.NewickFile(tree.getNewick()),
- tree.getTitle(), tree.getWidth(), tree.getHeight(),
- tree.getXpos(), tree.getYpos());
+ tp = af.showNewickTree(new NewickFile(tree.getNewick()),
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
if (tree.getId() != null)
{
// perhaps bind the tree id to something ?
@@ -3761,13 +3909,13 @@ public class Jalview2XML
// TODO: should check if tp has been manipulated by user - if so its
// settings shouldn't be modified
tp.setTitle(tree.getTitle());
- tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
- tree.getWidth(), tree.getHeight()));
- tp.av = av; // af.viewport; // TODO: verify 'associate with all
- // views'
- // works still
- tp.treeCanvas.av = av; // af.viewport;
- tp.treeCanvas.ap = ap; // af.alignPanel;
+ tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight())));
+ tp.setViewport(av); // af.viewport;
+ // TODO: verify 'associate with all views' works still
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
if (tp == null)
@@ -3777,29 +3925,31 @@ public class Jalview2XML
continue;
}
- tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
tp.fitToWindow_actionPerformed(null);
if (tree.getFontName() != null)
{
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),
- tree.getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(
+ new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
+ safeInt(tree.getFontSize())));
}
else
{
- tp.setTreeFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(
+ new Font(view.getFontName(), safeInt(view.getFontStyle()),
+ safeInt(view.getFontSize())));
}
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
+ tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
+ tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
+ tp.showDistances(safeBoolean(tree.isShowDistances()));
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
- if (tree.getCurrentTree())
+ if (safeBoolean(tree.isCurrentTree()))
{
- af.viewport.setCurrentTree(tp.getTree());
+ af.getViewport().setCurrentTree(tp.getTree());
}
}
@@ -3818,7 +3968,7 @@ public class Jalview2XML
* @param ap
*/
protected void loadPDBStructures(jarInputStreamProvider jprovider,
- JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
+ List jseqs, AlignFrame af, AlignmentPanel ap)
{
/*
* Run through all PDB ids on the alignment, and collect mappings between
@@ -3826,41 +3976,43 @@ public class Jalview2XML
*/
Map structureViewers = new LinkedHashMap<>();
- for (int i = 0; i < jseqs.length; i++)
+ for (int i = 0; i < jseqs.size(); i++)
{
- if (jseqs[i].getPdbidsCount() > 0)
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getPdbids().size() > 0)
{
- Pdbids[] ids = jseqs[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ List ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
{
- final int structureStateCount = ids[p].getStructureStateCount();
+ Pdbids pdbid = ids.get(p);
+ final int structureStateCount = pdbid.getStructureState().size();
for (int s = 0; s < structureStateCount; s++)
{
// check to see if we haven't already created this structure view
- final StructureState structureState = ids[p]
- .getStructureState(s);
+ final StructureState structureState = pdbid
+ .getStructureState().get(s);
String sviewid = (structureState.getViewId() == null) ? null
: structureState.getViewId() + uniqueSetSuffix;
jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
- // Originally : ids[p].getFile()
+ // Originally : pdbid.getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
- ids[p].getFile()));
- jpdb.setId(ids[p].getId());
+ jpdb.setFile(
+ loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
+ jpdb.setId(pdbid.getId());
- int x = structureState.getXpos();
- int y = structureState.getYpos();
- int width = structureState.getWidth();
- int height = structureState.getHeight();
+ int x = safeInt(structureState.getXpos());
+ int y = safeInt(structureState.getYpos());
+ int width = safeInt(structureState.getWidth());
+ int height = safeInt(structureState.getHeight());
// Probably don't need to do this anymore...
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
- ids[p].getFile());
+ String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile());
jalview.datamodel.SequenceI seq = seqRefIds
- .get(jseqs[i].getId() + "");
+ .get(jseq.getId() + "");
if (sviewid == null)
{
sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
@@ -3883,19 +4035,14 @@ public class Jalview2XML
// linkAlignPanel,superposeWithAlignpanel}} from hash
StructureViewerModel jmoldat = structureViewers.get(sviewid);
jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
- | (structureState.hasAlignwithAlignPanel()
- ? structureState.getAlignwithAlignPanel()
- : false));
+ || structureState.isAlignwithAlignPanel());
/*
* Default colour by linked panel to false if not specified (e.g.
* for pre-2.7 projects)
*/
boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
- colourWithAlignPanel |= (structureState
- .hasColourwithAlignPanel()
- ? structureState.getColourwithAlignPanel()
- : false);
+ colourWithAlignPanel |= structureState.isColourwithAlignPanel();
jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
/*
@@ -3903,27 +4050,23 @@ public class Jalview2XML
* pre-2.7 projects)
*/
boolean colourByViewer = jmoldat.isColourByViewer();
- colourByViewer &= structureState.hasColourByJmol()
- ? structureState.getColourByJmol()
- : true;
+ colourByViewer &= structureState.isColourByJmol();
jmoldat.setColourByViewer(colourByViewer);
if (jmoldat.getStateData().length() < structureState
- .getContent().length())
+ .getValue()/*Content()*/.length())
{
- {
- jmoldat.setStateData(structureState.getContent());
- }
+ jmoldat.setStateData(structureState.getValue());// Content());
}
- if (ids[p].getFile() != null)
+ if (pdbid.getFile() != null)
{
- File mapkey = new File(ids[p].getFile());
+ File mapkey = new File(pdbid.getFile());
StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
if (seqstrmaps == null)
{
jmoldat.getFileData().put(mapkey,
seqstrmaps = jmoldat.new StructureData(pdbFile,
- ids[p].getId()));
+ pdbid.getId()));
}
if (!seqstrmaps.getSeqList().contains(seq))
{
@@ -4418,46 +4561,47 @@ public class Jalview2XML
}
}
- AlignFrame loadViewport(String file, JSeq[] JSEQ,
+ AlignFrame loadViewport(String file, List JSEQ,
List hiddenSeqs, AlignmentI al,
- JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
+ JalviewModel jm, Viewport view, String uniqueSeqSetId,
String viewId, List autoAlan)
{
AlignFrame af = null;
- af = new AlignFrame(al, view.getWidth(), view.getHeight(),
- uniqueSeqSetId, viewId);
+ af = new AlignFrame(al, safeInt(view.getWidth()),
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId);
af.setFileName(file, FileFormat.Jalview);
- for (int i = 0; i < JSEQ.length; i++)
+ final AlignViewport viewport = af.getViewport();
+ for (int i = 0; i < JSEQ.size(); i++)
{
- af.viewport.setSequenceColour(
- af.viewport.getAlignment().getSequenceAt(i),
- new java.awt.Color(JSEQ[i].getColour()));
+ int colour = safeInt(JSEQ.get(i).getColour());
+ viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
+ new Color(colour));
}
if (al.hasSeqrep())
{
- af.getViewport().setColourByReferenceSeq(true);
- af.getViewport().setDisplayReferenceSeq(true);
+ viewport.setColourByReferenceSeq(true);
+ viewport.setDisplayReferenceSeq(true);
}
- af.viewport.setGatherViewsHere(view.getGatheredViews());
+ viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
if (view.getSequenceSetId() != null)
{
AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
- af.viewport.setSequenceSetId(uniqueSeqSetId);
+ viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
- af.viewport.setHistoryList(av.getHistoryList());
- af.viewport.setRedoList(av.getRedoList());
+ viewport.setHistoryList(av.getHistoryList());
+ viewport.setRedoList(av.getRedoList());
}
else
{
- viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ viewportsAdded.put(uniqueSeqSetId, viewport);
}
// TODO: check if this method can be called repeatedly without
// side-effects if alignpanel already registered.
@@ -4466,15 +4610,15 @@ public class Jalview2XML
// apply Hidden regions to view.
if (hiddenSeqs != null)
{
- for (int s = 0; s < JSEQ.length; s++)
+ for (int s = 0; s < JSEQ.size(); s++)
{
SequenceGroup hidden = new SequenceGroup();
boolean isRepresentative = false;
- for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ for (int r = 0; r < JSEQ.get(s).getHiddenSequences().size(); r++)
{
isRepresentative = true;
SequenceI sequenceToHide = al
- .getSequenceAt(JSEQ[s].getHiddenSequences(r));
+ .getSequenceAt(JSEQ.get(s).getHiddenSequences().get(r));
hidden.addSequence(sequenceToHide, false);
// remove from hiddenSeqs list so we don't try to hide it twice
hiddenSeqs.remove(sequenceToHide);
@@ -4483,56 +4627,59 @@ public class Jalview2XML
{
SequenceI representativeSequence = al.getSequenceAt(s);
hidden.addSequence(representativeSequence, false);
- af.viewport.hideRepSequences(representativeSequence, hidden);
+ viewport.hideRepSequences(representativeSequence, hidden);
}
}
SequenceI[] hseqs = hiddenSeqs
.toArray(new SequenceI[hiddenSeqs.size()]);
- af.viewport.hideSequence(hseqs);
+ viewport.hideSequence(hseqs);
}
// recover view properties and display parameters
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.viewport.setAbovePIDThreshold(view.getPidSelected());
- af.viewport.setThreshold(view.getPidThreshold());
-
- af.viewport.setColourText(view.getShowColourText());
-
- af.viewport.setConservationSelected(view.getConservationSelected());
- af.viewport.setIncrement(view.getConsThreshold());
- af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.setRightAlignIds(view.getRightAlignIds());
- af.viewport.setFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(), view.getFontSize()), true);
- ViewStyleI vs = af.viewport.getViewStyle();
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
+ viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
+ final int pidThreshold = safeInt(view.getPidThreshold());
+ viewport.setThreshold(pidThreshold);
+
+ viewport.setColourText(safeBoolean(view.isShowColourText()));
+
+ viewport
+ .setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
+ viewport.setIncrement(safeInt(view.getConsThreshold()));
+ viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
+ viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
+ viewport.setFont(new Font(view.getFontName(),
+ safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
+ true);
+ ViewStyleI vs = viewport.getViewStyle();
vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
- af.viewport.setViewStyle(vs);
+ 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());
- af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
+ viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
+ viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
- af.viewport.setShowBoxes(view.getShowBoxes());
+ viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
- af.viewport.setShowText(view.getShowText());
+ viewport.setShowText(safeBoolean(view.isShowText()));
- af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
- af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
- af.viewport.setThresholdTextColour(view.getTextColThreshold());
- af.viewport.setShowUnconserved(
- view.hasShowUnconserved() ? view.isShowUnconserved() : false);
- af.viewport.getRanges().setStartRes(view.getStartRes());
+ viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
+ viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
+ viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
+ viewport.setShowUnconserved(view.isShowUnconserved());
+ viewport.getRanges().setStartRes(safeInt(view.getStartRes()));
if (view.getViewName() != null)
{
- af.viewport.viewName = view.getViewName();
+ viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
+ af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
@@ -4541,12 +4688,12 @@ public class Jalview2XML
{
if (view.getBgColour().startsWith("ucs"))
{
- cs = getUserColourScheme(jms, view.getBgColour());
+ cs = getUserColourScheme(jm, view.getBgColour());
}
else if (view.getBgColour().startsWith("Annotation"))
{
- AnnotationColours viewAnnColour = view.getAnnotationColours();
- cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
+ AnnotationColourScheme viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jm, true);
// annpos
@@ -4557,114 +4704,66 @@ public class Jalview2XML
}
}
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
- view.getIgnoreGapsinConsensus());
- af.viewport.getResidueShading()
- .setConsensus(af.viewport.getSequenceConsensusHash());
- af.viewport.setColourAppliesToAllGroups(false);
+ viewport.setGlobalColourScheme(cs);
+ viewport.getResidueShading().setThreshold(pidThreshold,
+ view.isIgnoreGapsinConsensus());
+ viewport.getResidueShading()
+ .setConsensus(viewport.getSequenceConsensusHash());
+ viewport.setColourAppliesToAllGroups(false);
- if (view.getConservationSelected() && cs != null)
+ if (safeBoolean(view.isConservationSelected()) && cs != null)
{
- af.viewport.getResidueShading()
- .setConservationInc(view.getConsThreshold());
+ viewport.getResidueShading()
+ .setConservationInc(safeInt(view.getConsThreshold()));
}
af.changeColour(cs);
- af.viewport.setColourAppliesToAllGroups(true);
+ viewport.setColourAppliesToAllGroups(true);
- af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+ viewport
+ .setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
- if (view.hasCentreColumnLabels())
- {
- af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
- }
- if (view.hasIgnoreGapsinConsensus())
- {
- af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
- null);
- }
- if (view.hasFollowHighlight())
- {
- af.viewport.setFollowHighlight(view.getFollowHighlight());
- }
- if (view.hasFollowSelection())
- {
- af.viewport.followSelection = view.getFollowSelection();
- }
- if (view.hasShowConsensusHistogram())
- {
- af.viewport
- .setShowConsensusHistogram(view.getShowConsensusHistogram());
- }
- else
- {
- af.viewport.setShowConsensusHistogram(true);
- }
- if (view.hasShowSequenceLogo())
- {
- af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
- }
- else
- {
- af.viewport.setShowSequenceLogo(false);
- }
- if (view.hasNormaliseSequenceLogo())
- {
- af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
- }
- if (view.hasShowDbRefTooltip())
- {
- af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
- }
- if (view.hasShowNPfeatureTooltip())
- {
- af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
- }
- if (view.hasShowGroupConsensus())
- {
- af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
- }
- else
- {
- af.viewport.setShowGroupConsensus(false);
- }
- if (view.hasShowGroupConservation())
- {
- af.viewport.setShowGroupConservation(view.getShowGroupConservation());
- }
- else
- {
- af.viewport.setShowGroupConservation(false);
- }
+ viewport.setCentreColumnLabels(view.isCentreColumnLabels());
+ viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
+ viewport.setFollowHighlight(view.isFollowHighlight());
+ viewport.followSelection = view.isFollowSelection();
+ viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
+ viewport.setShowSequenceLogo(view.isShowSequenceLogo());
+ viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
+ viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
+ viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
+ viewport.setShowGroupConsensus(view.isShowGroupConsensus());
+ viewport.setShowGroupConservation(view.isShowGroupConservation());
// recover feature settings
- if (jms.getFeatureSettings() != null)
+ if (jm.getFeatureSettings() != null)
{
FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
FeaturesDisplayed fdi;
- af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jms.getFeatureSettings()
- .getSettingCount()];
+ viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ String[] renderOrder = new String[jm.getFeatureSettings()
+ .getSetting().size()];
Map featureColours = new Hashtable<>();
Map featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jms.getFeatureSettings()
- .getSettingCount(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings()
+ .getSetting().size(); fs++)
{
- Setting setting = jms.getFeatureSettings().getSetting(fs);
+ Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
/*
* restore feature filters (if any)
*/
- MatcherSet filters = setting.getMatcherSet();
+ jalview.xml.binding.jalview.FeatureMatcherSet filters = setting
+ .getMatcherSet();
if (filters != null)
{
FeatureMatcherSetI filter = Jalview2XML
- .unmarshalFilter(featureType, filters);
+ .parseFilter(featureType, filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
@@ -4675,13 +4774,13 @@ public class Jalview2XML
* restore feature colour scheme
*/
Color maxColour = new Color(setting.getColour());
- if (setting.hasMincolour())
+ if (setting.getMincolour() != null)
{
/*
* minColour is always set unless a simple colour
* (including for colour by label though it doesn't use it)
*/
- Color minColour = new Color(setting.getMincolour());
+ Color minColour = new Color(setting.getMincolour().intValue());
Color noValueColour = minColour;
NoValueColour noColour = setting.getNoValueColour();
if (noColour == NoValueColour.NONE)
@@ -4692,18 +4791,20 @@ public class Jalview2XML
{
noValueColour = maxColour;
}
- float min = setting.hasMin() ? setting.getMin() : 0f;
- float max = setting.hasMin() ? setting.getMax() : 1f;
+ float min = safeFloat(safeFloat(setting.getMin()));
+ float max = setting.getMax() == null ? 1f
+ : setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(minColour, maxColour,
noValueColour, min, max);
- if (setting.getAttributeNameCount() > 0)
+ if (setting.getAttributeName().size() > 0)
{
- gc.setAttributeName(setting.getAttributeName());
+ gc.setAttributeName(setting.getAttributeName().toArray(
+ new String[setting.getAttributeName().size()]));
}
- if (setting.hasThreshold())
+ if (setting.getThreshold() != null)
{
- gc.setThreshold(setting.getThreshold());
- int threshstate = setting.getThreshstate();
+ gc.setThreshold(setting.getThreshold().floatValue());
+ int threshstate = safeInt(setting.getThreshstate());
// -1 = None, 0 = Below, 1 = Above threshold
if (threshstate == 0)
{
@@ -4715,13 +4816,13 @@ public class Jalview2XML
}
}
gc.setAutoScaled(true); // default
- if (setting.hasAutoScale())
+ if (setting.isAutoScale() != null)
{
- gc.setAutoScaled(setting.getAutoScale());
+ gc.setAutoScaled(setting.isAutoScale());
}
- if (setting.hasColourByLabel())
+ if (setting.isColourByLabel() != null)
{
- gc.setColourByLabel(setting.getColourByLabel());
+ gc.setColourByLabel(setting.isColourByLabel());
}
// and put in the feature colour table.
featureColours.put(featureType, gc);
@@ -4732,25 +4833,25 @@ public class Jalview2XML
new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
- if (setting.hasOrder())
+ if (setting.getOrder() != null)
{
- featureOrder.put(featureType, setting.getOrder());
+ featureOrder.put(featureType, setting.getOrder().floatValue());
}
else
{
featureOrder.put(featureType, new Float(
- fs / jms.getFeatureSettings().getSettingCount()));
+ fs / jm.getFeatureSettings().getSetting().size()));
}
- if (setting.getDisplay())
+ if (safeBoolean(setting.isDisplay()))
{
fdi.setVisible(featureType);
}
}
Map fgtable = new Hashtable<>();
- for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
+ for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
{
- Group grp = jms.getFeatureSettings().getGroup(gs);
- fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
+ Group grp = jm.getFeatureSettings().getGroup().get(gs);
+ fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
}
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
@@ -4760,13 +4861,13 @@ public class Jalview2XML
fr.transferSettings(frs);
}
- if (view.getHiddenColumnsCount() > 0)
+ if (view.getHiddenColumns().size() > 0)
{
- for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+ for (int c = 0; c < view.getHiddenColumns().size(); c++)
{
- af.viewport.hideColumns(view.getHiddenColumns(c).getStart(),
- view.getHiddenColumns(c).getEnd() // +1
- );
+ final HiddenColumns hc = view.getHiddenColumns().get(c);
+ viewport.hideColumns(safeInt(hc.getStart()),
+ safeInt(hc.getEnd()) /* +1 */);
}
}
if (view.getCalcIdParam() != null)
@@ -4775,7 +4876,7 @@ public class Jalview2XML
{
if (calcIdParam != null)
{
- if (recoverCalcIdParam(calcIdParam, af.viewport))
+ if (recoverCalcIdParam(calcIdParam, viewport))
{
}
else
@@ -4786,7 +4887,7 @@ public class Jalview2XML
}
}
}
- af.setMenusFromViewport(af.viewport);
+ af.setMenusFromViewport(viewport);
af.setTitle(view.getTitle());
// TODO: we don't need to do this if the viewport is aready visible.
/*
@@ -4797,8 +4898,8 @@ public class Jalview2XML
String complementaryViewId = view.getComplementId();
if (complementaryViewId == null)
{
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
- view.getHeight());
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
@@ -4817,16 +4918,17 @@ public class Jalview2XML
* @param viewAnnColour
* @param af
* @param al
- * @param jms
+ * @param model
* @param checkGroupAnnColour
* @return
*/
private ColourSchemeI constructAnnotationColour(
- AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
- JalviewModelSequence jms, boolean checkGroupAnnColour)
+ AnnotationColourScheme viewAnnColour, AlignFrame af,
+ AlignmentI al, JalviewModel model, boolean checkGroupAnnColour)
{
boolean propagateAnnColour = false;
- AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
+ AlignmentI annAlignment = af != null ? af.getViewport().getAlignment()
+ : al;
if (checkGroupAnnColour && al.getGroups() != null
&& al.getGroups().size() > 0)
{
@@ -4872,34 +4974,36 @@ public class Jalview2XML
}
if (matchedAnnotation.getThreshold() == null)
{
- matchedAnnotation.setThreshold(new GraphLine(
- viewAnnColour.getThreshold(), "Threshold", Color.black));
+ matchedAnnotation.setThreshold(
+ new GraphLine(safeFloat(viewAnnColour.getThreshold()),
+ "Threshold", Color.black));
}
AnnotationColourGradient cs = null;
if (viewAnnColour.getColourScheme().equals("None"))
{
cs = new AnnotationColourGradient(matchedAnnotation,
- new Color(viewAnnColour.getMinColour()),
- new Color(viewAnnColour.getMaxColour()),
- viewAnnColour.getAboveThreshold());
+ new Color(safeInt(viewAnnColour.getMinColour())),
+ new Color(safeInt(viewAnnColour.getMaxColour())),
+ safeInt(viewAnnColour.getAboveThreshold()));
}
else if (viewAnnColour.getColourScheme().startsWith("ucs"))
{
cs = new AnnotationColourGradient(matchedAnnotation,
- getUserColourScheme(jms, viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
+ getUserColourScheme(model, viewAnnColour.getColourScheme()),
+ safeInt(viewAnnColour.getAboveThreshold()));
}
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
ColourSchemeProperty.getColourScheme(al,
viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
+ safeInt(viewAnnColour.getAboveThreshold()));
}
- boolean perSequenceOnly = viewAnnColour.isPerSequence();
- boolean useOriginalColours = viewAnnColour.isPredefinedColours();
+ boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence());
+ boolean useOriginalColours = safeBoolean(
+ viewAnnColour.isPredefinedColours());
cs.setSeqAssociated(perSequenceOnly);
cs.setPredefinedColours(useOriginalColours);
@@ -4916,7 +5020,7 @@ public class Jalview2XML
AnnotationColourGradient groupScheme = new AnnotationColourGradient(
matchedAnnotation, sg.getColourScheme(),
- viewAnnColour.getAboveThreshold());
+ safeInt(viewAnnColour.getAboveThreshold()));
sg.setColourScheme(groupScheme);
groupScheme.setSeqAssociated(perSequenceOnly);
groupScheme.setPredefinedColours(useOriginalColours);
@@ -5050,10 +5154,8 @@ public class Jalview2XML
{
return false;
}
- String id;
- if (skipList.containsKey(
- id = object.getJalviewModelSequence().getViewport()[0]
- .getSequenceSetId()))
+ String id = object.getViewport().get(0).getSequenceSetId();
+ if (skipList.containsKey(id))
{
if (Cache.log != null && Cache.log.isDebugEnabled())
{
@@ -5093,9 +5195,9 @@ public class Jalview2XML
// create a list of new dataset sequences
dseqs = new Vector();
}
- for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
+ for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
{
- Sequence vamsasSeq = vamsasSet.getSequence(i);
+ Sequence vamsasSeq = vamsasSet.getSequence().get(i);
ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
}
// create a new dataset
@@ -5338,13 +5440,11 @@ public class Jalview2XML
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
- for (int d = 0; d < sequence.getDBRefCount(); d++)
+ for (int d = 0; d < sequence.getDBRef().size(); d++)
{
- DBRef dr = sequence.getDBRef(d);
+ DBRef dr = sequence.getDBRef().get(d);
jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- sequence.getDBRef(d).getSource(),
- sequence.getDBRef(d).getVersion(),
- sequence.getDBRef(d).getAccessionId());
+ dr.getSource(), dr.getVersion(), dr.getAccessionId());
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
@@ -5357,88 +5457,88 @@ public class Jalview2XML
{
SequenceI dsto = null;
// Mapping m = dr.getMapping();
- int fr[] = new int[m.getMapListFromCount() * 2];
- Enumeration f = m.enumerateMapListFrom();
- for (int _i = 0; f.hasMoreElements(); _i += 2)
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator from = m.getMapListFrom().iterator();// enumerateMapListFrom();
+ for (int _i = 0; from.hasNext(); _i += 2)
{
- MapListFrom mf = (MapListFrom) f.nextElement();
+ MapListFrom mf = from.next();
fr[_i] = mf.getStart();
fr[_i + 1] = mf.getEnd();
}
- int fto[] = new int[m.getMapListToCount() * 2];
- f = m.enumerateMapListTo();
- for (int _i = 0; f.hasMoreElements(); _i += 2)
+ int fto[] = new int[m.getMapListTo().size() * 2];
+ Iterator to = m.getMapListTo().iterator();// enumerateMapListTo();
+ for (int _i = 0; to.hasNext(); _i += 2)
{
- MapListTo mf = (MapListTo) f.nextElement();
+ MapListTo mf = to.next();
fto[_i] = mf.getStart();
fto[_i + 1] = mf.getEnd();
}
jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
- fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
- if (m.getMappingChoice() != null)
+ fto, m.getMapFromUnit().intValue(),
+ m.getMapToUnit().intValue());
+ // if (m.getMappingChoice() != null)
+ // {
+ // MappingChoice mc = m.getMappingChoice();
+ if (m.getDseqFor() != null)
{
- MappingChoice mc = m.getMappingChoice();
- if (mc.getDseqFor() != null)
+ String dsfor = m.getDseqFor();
+ if (seqRefIds.containsKey(dsfor))
{
- String dsfor = "" + mc.getDseqFor();
- if (seqRefIds.containsKey(dsfor))
- {
- /**
- * recover from hash
- */
- jmap.setTo(seqRefIds.get(dsfor));
- }
- else
- {
- frefedSequence.add(newMappingRef(dsfor, jmap));
- }
+ /**
+ * recover from hash
+ */
+ jmap.setTo(seqRefIds.get(dsfor));
}
else
{
- /**
- * local sequence definition
+ frefedSequence.add(newMappingRef(dsfor, jmap));
+ }
+ }
+ else
+ {
+ /**
+ * local sequence definition
+ */
+ Sequence ms = m.getSequence();
+ SequenceI djs = null;
+ String sqid = ms.getDsseqid();
+ if (sqid != null && sqid.length() > 0)
+ {
+ /*
+ * recover dataset sequence
*/
- Sequence ms = mc.getSequence();
- SequenceI djs = null;
- String sqid = ms.getDsseqid();
- if (sqid != null && sqid.length() > 0)
- {
- /*
- * recover dataset sequence
- */
- djs = seqRefIds.get(sqid);
- }
- else
- {
- System.err.println(
- "Warning - making up dataset sequence id for DbRef sequence map reference");
- sqid = ((Object) ms).toString(); // make up a new hascode for
- // undefined dataset sequence hash
- // (unlikely to happen)
- }
-
- if (djs == null)
- {
- /**
- * make a new dataset sequence and add it to refIds hash
- */
- djs = new jalview.datamodel.Sequence(ms.getName(),
- ms.getSequence());
- djs.setStart(jmap.getMap().getToLowest());
- djs.setEnd(jmap.getMap().getToHighest());
- djs.setVamsasId(uniqueSetSuffix + sqid);
- jmap.setTo(djs);
- incompleteSeqs.put(sqid, djs);
- seqRefIds.put(sqid, djs);
+ djs = seqRefIds.get(sqid);
+ }
+ else
+ {
+ System.err.println(
+ "Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object) ms).toString(); // make up a new hascode for
+ // undefined dataset sequence hash
+ // (unlikely to happen)
+ }
- }
- jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
- addDBRefs(djs, ms);
+ if (djs == null)
+ {
+ /**
+ * make a new dataset sequence and add it to refIds hash
+ */
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
+ djs.setStart(jmap.getMap().getToLowest());
+ djs.setEnd(jmap.getMap().getToHighest());
+ djs.setVamsasId(uniqueSetSuffix + sqid);
+ jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
+ seqRefIds.put(sqid, djs);
}
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
}
- return (jmap);
+ return jmap;
}
/**
@@ -5454,7 +5554,8 @@ public class Jalview2XML
JalviewModel jm = saveState(ap, null, null, null);
uniqueSetSuffix = "";
- jm.getJalviewModelSequence().getViewport(0).setId(null);
+ // jm.getJalviewModelSequence().getViewport(0).setId(null);
+ jm.getViewport().get(0).setId(null);
// we don't overwrite the view we just copied
if (this.frefedSequence == null)
@@ -5465,7 +5566,7 @@ public class Jalview2XML
viewportsAdded.clear();
AlignFrame af = loadFromObject(jm, null, false, null);
- af.alignPanels.clear();
+ af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
/*
@@ -5719,10 +5820,10 @@ public class Jalview2XML
* @param fcol
* @return
*/
- protected static jalview.schemabinding.version2.Colour marshalColour(
+ public static Colour marshalColour(
String featureType, FeatureColourI fcol)
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ Colour col = new Colour();
if (fcol.isSimpleColour())
{
col.setRGB(Format.getHexString(fcol.getColour()));
@@ -5736,12 +5837,17 @@ public class Jalview2XML
col.setAutoScale(fcol.isAutoScaled());
col.setThreshold(fcol.getThreshold());
col.setColourByLabel(fcol.isColourByLabel());
- col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE
- : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW
- : ColourThreshTypeType.NONE));
+ col.setThreshType(fcol.isAboveThreshold() ? ThresholdType.ABOVE
+ : (fcol.isBelowThreshold() ? ThresholdType.BELOW
+ : ThresholdType.NONE));
if (fcol.isColourByAttribute())
{
- col.setAttributeName(fcol.getAttributeName());
+ final String[] attName = fcol.getAttributeName();
+ col.getAttributeName().add(attName[0]);
+ if (attName.length > 1)
+ {
+ col.getAttributeName().add(attName[1]);
+ }
}
Color noColour = fcol.getNoColour();
if (noColour == null)
@@ -5771,10 +5877,11 @@ public class Jalview2XML
* @param and
* if true, conditions are and-ed, else or-ed
*/
- protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher,
- Iterator filters, boolean and)
+ public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
+ FeatureMatcherI firstMatcher, Iterator filters,
+ boolean and)
{
- MatcherSet result = new MatcherSet();
+ jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
if (filters.hasNext())
{
@@ -5783,12 +5890,15 @@ public class Jalview2XML
*/
CompoundMatcher compound = new CompoundMatcher();
compound.setAnd(and);
- MatcherSet matcher1 = marshalFilter(firstMatcher,
- Collections.emptyIterator(), and);
- compound.addMatcherSet(matcher1);
+ jalview.xml.binding.jalview.FeatureMatcherSet matcher1 = marshalFilter(
+ firstMatcher, Collections.emptyIterator(), and);
+ // compound.addMatcherSet(matcher1);
+ compound.getMatcherSet().add(matcher1);
FeatureMatcherI nextMatcher = filters.next();
- MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and);
- compound.addMatcherSet(matcher2);
+ jalview.xml.binding.jalview.FeatureMatcherSet matcher2 = marshalFilter(
+ nextMatcher, filters, and);
+ // compound.addMatcherSet(matcher2);
+ compound.getMatcherSet().add(matcher2);
result.setCompoundMatcher(compound);
}
else
@@ -5796,22 +5906,29 @@ public class Jalview2XML
/*
* single condition matcher
*/
- MatchCondition matcherModel = new MatchCondition();
+ // MatchCondition matcherModel = new MatchCondition();
+ jalview.xml.binding.jalview.FeatureMatcher matcherModel = new jalview.xml.binding.jalview.FeatureMatcher();
matcherModel.setCondition(
firstMatcher.getMatcher().getCondition().getStableName());
matcherModel.setValue(firstMatcher.getMatcher().getPattern());
if (firstMatcher.isByAttribute())
{
- matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE);
- matcherModel.setAttributeName(firstMatcher.getAttribute());
+ matcherModel.setBy(FilterBy.BY_ATTRIBUTE);
+ // matcherModel.setAttributeName(firstMatcher.getAttribute());
+ String[] attName = firstMatcher.getAttribute();
+ matcherModel.getAttributeName().add(attName[0]); // attribute
+ if (attName.length > 1)
+ {
+ matcherModel.getAttributeName().add(attName[1]); // sub-attribute
+ }
}
else if (firstMatcher.isByLabel())
{
- matcherModel.setBy(FeatureMatcherByType.BYLABEL);
+ matcherModel.setBy(FilterBy.BY_LABEL);
}
else if (firstMatcher.isByScore())
{
- matcherModel.setBy(FeatureMatcherByType.BYSCORE);
+ matcherModel.setBy(FilterBy.BY_SCORE);
}
result.setMatchCondition(matcherModel);
}
@@ -5826,13 +5943,14 @@ public class Jalview2XML
* @param matcherSetModel
* @return
*/
- protected static FeatureMatcherSetI unmarshalFilter(
- String featureType, MatcherSet matcherSetModel)
+ public static FeatureMatcherSetI parseFilter(
+ String featureType,
+ jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
{
FeatureMatcherSetI result = new FeatureMatcherSet();
try
{
- unmarshalFilterConditions(result, matcherSetModel, true);
+ parseFilterConditions(result, matcherSetModel, true);
} catch (IllegalStateException e)
{
// mixing AND and OR conditions perhaps
@@ -5856,32 +5974,36 @@ public class Jalview2XML
* @throws IllegalStateException
* if AND and OR conditions are mixed
*/
- protected static void unmarshalFilterConditions(
- FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel,
+ protected static void parseFilterConditions(
+ FeatureMatcherSetI matcherSet,
+ jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
boolean and)
{
- MatchCondition mc = matcherSetModel.getMatchCondition();
+ jalview.xml.binding.jalview.FeatureMatcher mc = matcherSetModel
+ .getMatchCondition();
if (mc != null)
{
/*
* single condition
*/
- FeatureMatcherByType filterBy = mc.getBy();
+ FilterBy filterBy = mc.getBy();
Condition cond = Condition.fromString(mc.getCondition());
String pattern = mc.getValue();
FeatureMatcherI matchCondition = null;
- if (filterBy == FeatureMatcherByType.BYLABEL)
+ if (filterBy == FilterBy.BY_LABEL)
{
matchCondition = FeatureMatcher.byLabel(cond, pattern);
}
- else if (filterBy == FeatureMatcherByType.BYSCORE)
+ else if (filterBy == FilterBy.BY_SCORE)
{
matchCondition = FeatureMatcher.byScore(cond, pattern);
}
- else if (filterBy == FeatureMatcherByType.BYATTRIBUTE)
+ else if (filterBy == FilterBy.BY_ATTRIBUTE)
{
- String[] attNames = mc.getAttributeName();
+ final List attributeName = mc.getAttributeName();
+ String[] attNames = attributeName
+ .toArray(new String[attributeName.size()]);
matchCondition = FeatureMatcher.byAttribute(cond, pattern,
attNames);
}
@@ -5904,13 +6026,13 @@ public class Jalview2XML
/*
* compound condition
*/
- MatcherSet[] matchers = matcherSetModel.getCompoundMatcher()
- .getMatcherSet();
- boolean anded = matcherSetModel.getCompoundMatcher().getAnd();
- if (matchers.length == 2)
+ List matchers = matcherSetModel
+ .getCompoundMatcher().getMatcherSet();
+ boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
+ if (matchers.size() == 2)
{
- unmarshalFilterConditions(matcherSet, matchers[0], anded);
- unmarshalFilterConditions(matcherSet, matchers[1], anded);
+ parseFilterConditions(matcherSet, matchers.get(0), anded);
+ parseFilterConditions(matcherSet, matchers.get(1), anded);
}
else
{
@@ -5925,12 +6047,11 @@ public class Jalview2XML
* @param colourModel
* @return
*/
- protected static FeatureColourI unmarshalColour(
- jalview.schemabinding.version2.Colour colourModel)
+ public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
- if (colourModel.hasMax())
+ if (colourModel.getMax() != null)
{
Color mincol = null;
Color maxcol = null;
@@ -5956,36 +6077,36 @@ public class Jalview2XML
}
colour = new FeatureColour(mincol, maxcol, noValueColour,
- colourModel.getMin(),
- colourModel.getMax());
- String[] attributes = colourModel.getAttributeName();
+ safeFloat(colourModel.getMin()),
+ safeFloat(colourModel.getMax()));
+ final List attributeName = colourModel.getAttributeName();
+ String[] attributes = attributeName
+ .toArray(new String[attributeName.size()]);
if (attributes != null && attributes.length > 0)
{
colour.setAttributeName(attributes);
}
- if (colourModel.hasAutoScale())
+ if (colourModel.isAutoScale() != null)
{
- colour.setAutoScaled(colourModel.getAutoScale());
+ colour.setAutoScaled(colourModel.isAutoScale().booleanValue());
}
- if (colourModel.hasColourByLabel())
+ if (colourModel.isColourByLabel() != null)
{
- colour.setColourByLabel(colourModel.getColourByLabel());
+ colour.setColourByLabel(
+ colourModel.isColourByLabel().booleanValue());
}
- if (colourModel.hasThreshold())
+ if (colourModel.getThreshold() != null)
{
- colour.setThreshold(colourModel.getThreshold());
+ colour.setThreshold(colourModel.getThreshold().floatValue());
}
- ColourThreshTypeType ttyp = colourModel.getThreshType();
- if (ttyp != null)
+ ThresholdType ttyp = colourModel.getThreshType();
+ if (ttyp == ThresholdType.ABOVE)
{
- if (ttyp == ColourThreshTypeType.ABOVE)
- {
- colour.setAboveThreshold(true);
- }
- else if (ttyp == ColourThreshTypeType.BELOW)
- {
- colour.setBelowThreshold(true);
- }
+ colour.setAboveThreshold(true);
+ }
+ else if (ttyp == ThresholdType.BELOW)
+ {
+ colour.setBelowThreshold(true);
}
}
else