*/
package jalview.project;
+import static jalview.math.RotatableMatrix.Axis.X;
+import static jalview.math.RotatableMatrix.Axis.Y;
+import static jalview.math.RotatableMatrix.Axis.Z;
+
import jalview.analysis.Conservation;
+import jalview.analysis.PCA;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.gui.ChimeraViewFrame;
import jalview.gui.Desktop;
import jalview.gui.FeatureRenderer;
-import jalview.gui.Jalview2XML_V1;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+import jalview.gui.PCAPanel;
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.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.HMMFile;
+import jalview.io.NewickFile;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
-import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.PreferredServiceRegistry;
import jalview.ws.jws2.dm.AAConSettings;
-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.Annotation.ThresholdLine;
import jalview.xml.binding.jalview.AnnotationColourScheme;
import jalview.xml.binding.jalview.AnnotationElement;
+import jalview.xml.binding.jalview.DoubleMatrix;
+import jalview.xml.binding.jalview.DoubleVector;
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.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.PcaViewer;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
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.Mapping;
import jalview.xml.binding.jalview.NoValueColour;
import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.PcaDataType;
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.VAMSAS;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStream;
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;
*/
public class Jalview2XML
{
+
+ // BH 2018 we add the .jvp binary extension to J2S so that
+ // it will declare that binary when we do the file save from the browser
+
+ static
+ {
+ Platform.addJ2SBinaryType(".jvp?");
+ }
+
private static final String VIEWER_PREFIX = "viewer_";
private static final String RNA_PREFIX = "rna_";
+ private static final String HMMER_PREFIX = "hmmer_";
+
private static final String UTF_8 = "UTF-8";
+ /**
+ * prefix for recovering datasets for alignments with multiple views where
+ * non-existent dataset IDs were written for some views
+ */
+ private static final String UNIQSEQSETID = "uniqueSeqSetId.";
+
// use this with nextCounter() to make unique names for entities
private int counter = 0;
private Map<RnaModel, String> rnaSessions = new HashMap<>();
/**
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = false;
+
+ /*
+ * JalviewJS only -- to allow read file bytes to be saved in the
+ * created AlignFrame, allowing File | Reload of a project file to work
+ *
+ * BH 2019 JAL-3436
+ */
+ private File jarFile;
+
+ /**
+ * 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
* @param _jmap
* @return
*/
- public SeqFref newMappingRef(final String sref,
+ protected SeqFref newMappingRef(final String sref,
final jalview.datamodel.Mapping _jmap)
{
SeqFref fref = new SeqFref(sref, "Mapping")
return fref;
}
- public SeqFref newAlcodMapRef(final String sref,
+ protected SeqFref newAlcodMapRef(final String sref,
final AlignedCodonFrame _cf,
final jalview.datamodel.Mapping _jmap)
{
public boolean isResolvable()
{
return super.isResolvable() && mp.getTo() != null;
- };
+ }
@Override
boolean resolve()
return fref;
}
- public void resolveFrefedSequences()
+ protected void resolveFrefedSequences()
{
Iterator<SeqFref> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
public void saveState(File statefile)
{
FileOutputStream fos = null;
+
try
{
+
fos = new FileOutputStream(statefile);
+
JarOutputStream jout = new JarOutputStream(fos);
saveState(jout);
+ fos.close();
} catch (Exception e)
{
+ Cache.log.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
{
- errorMessage = "Couldn't write Jalview Archive to output file '"
+ errorMessage = "Did't write Jalview Archive to output file '"
+ statefile + "' - See console error log for details";
}
else
{
- errorMessage += "(output file was '" + statefile + "')";
+ errorMessage += "(Didn't write Jalview Archive to output file '"
+ + statefile + ")";
}
e.printStackTrace();
} finally
* core method for storing state for a set of AlignFrames.
*
* @param frames
- * - frames involving all data to be exported (including containing
- * splitframes)
+ * - frames involving all data to be exported (including those
+ * contained in splitframes, though not the split frames themselves)
* @param jout
* - project output stream
*/
private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
{
+
Hashtable<String, AlignFrame> dsses = new Hashtable<>();
/*
for (int i = frames.size() - 1; i > -1; i--)
{
AlignFrame af = frames.get(i);
+ AlignViewport vp = af.getViewport();
// skip ?
if (skipList != null && skipList
- .containsKey(af.getViewport().getSequenceSetId()))
+ .containsKey(vp.getSequenceSetId()))
{
continue;
}
String shortName = makeFilename(af, shortNames);
- int apSize = af.getAlignPanels().size();
-
+ AlignmentI alignment = vp.getAlignment();
+ List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
+ int apSize = panels.size();
for (int ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
- .get(ap);
+ {
+ AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
String fileName = apSize == 1 ? shortName : ap + shortName;
if (!fileName.endsWith(".xml"))
{
}
saveState(apanel, fileName, jout, viewIds);
-
- String dssid = getDatasetIdRef(
- af.getViewport().getAlignment().getDataset());
+ }
+ if (apSize > 0)
+ {
+ // BH moved next bit out of inner loop, not that it really matters.
+ // so we are testing to make sure we actually have an alignment,
+ // apparently.
+ String dssid = getDatasetIdRef(alignment.getDataset());
if (!dsses.containsKey(dssid))
{
+ // We have not already covered this data by reference from another
+ // frame.
dsses.put(dssid, af);
}
}
} catch (Exception foo)
{
}
- ;
jout.close();
} catch (Exception ex)
{
{
try
{
- FileOutputStream fos = new FileOutputStream(jarFile);
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
+ FileOutputStream fos = new FileOutputStream(doBackup ?
+ backupfiles.getTempFilePath() : jarFile);
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
} catch (Exception foo)
{
}
- ;
jout.close();
- return true;
+ boolean success = true;
+
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(success);
+ success = backupfiles.rollBackupsAndRenameTempFile();
+ }
+
+ return success;
} catch (Exception ex)
{
errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
}
}
+ /**
+ * Each AlignFrame has a single data set associated with it. Note that none of
+ * these frames are split frames, because Desktop.getAlignFrames() collects
+ * top and bottom separately here.
+ *
+ * @param dsses
+ * @param fileName
+ * @param jout
+ */
private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
String fileName, JarOutputStream jout)
{
+ // Note that in saveAllFrames we have associated each specific dataset to
+ // ONE of its associated frames.
+
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
JarOutputStream jout, List<String> viewIds)
{
return saveState(ap, fileName, false, jout, viewIds);
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
boolean storeDS, JarOutputStream jout, List<String> viewIds)
{
if (viewIds == null)
jseq.getFeatures().add(features);
}
+ /*
+ * save PDB entries for sequence
+ */
if (jdatasq.getAllPDBEntries() != null)
{
Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
* only view *should* be coped with sensibly.
*/
// This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
+ if (jds.hasHMMProfile())
+ {
+ saveHmmerProfile(jout, jseq, jds);
+ }
+
// jms.addJSeq(jseq);
object.getJSeq().add(jseq);
}
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int t = 0; t < frames.length; t++)
{
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
tree.setId(makeHashCode(tp, null));
+ tree.setLinkToAllViews(
+ tp.getTreeCanvas().isApplyToAllViews());
+
// jms.addTree(tree);
object.getTree().add(tree);
}
}
}
+ /*
+ * save PCA viewers
+ */
+ if (!storeDS && Desktop.getDesktopPane() != null)
+ {
+ for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
+ {
+ if (frame instanceof PCAPanel)
+ {
+ PCAPanel panel = (PCAPanel) frame;
+ if (panel.getAlignViewport().getAlignment() == jal)
+ {
+ savePCA(panel, object);
+ }
+ }
+ }
+ }
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
view.setFollowHighlight(av.isFollowHighlight());
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ view.setShowComplementFeatures(av.isShowComplementFeatures());
+ view.setShowComplementFeaturesOnTop(
+ av.isShowComplementFeaturesOnTop());
if (av.getFeaturesDisplayed() != null)
{
FeatureSettings fs = new FeatureSettings();
- FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+ FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
.getFeatureRenderer();
String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
// using save and then load
try
{
+ fileName = fileName.replace('\\', '/');
System.out.println("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
}
return object;
}
+ /**
+ * Saves the HMMER profile associated with the sequence as a file in the jar,
+ * in HMMER format, and saves the name of the file as a child element of the
+ * XML sequence element
+ *
+ * @param jout
+ * @param xmlSeq
+ * @param seq
+ */
+ protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+ SequenceI seq)
+ {
+ HiddenMarkovModel profile = seq.getHMM();
+ if (profile == null)
+ {
+ warn("Want to save HMM profile for " + seq.getName()
+ + " but none found");
+ return;
+ }
+ HMMFile hmmFile = new HMMFile(profile);
+ String hmmAsString = hmmFile.print();
+ String jarEntryName = HMMER_PREFIX + nextCounter();
+ try
+ {
+ writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+ xmlSeq.setHmmerProfile(jarEntryName);
+ } catch (IOException e)
+ {
+ warn("Error saving HMM profile: " + e.getMessage());
+ }
+ }
+
+
+ /**
+ * Writes PCA viewer attributes and computed values to an XML model object and
+ * adds it to the JalviewModel. Any exceptions are reported by logging.
+ */
+ protected void savePCA(PCAPanel panel, JalviewModel object)
+ {
+ try
+ {
+ PcaViewer viewer = new PcaViewer();
+ viewer.setHeight(panel.getHeight());
+ viewer.setWidth(panel.getWidth());
+ viewer.setXpos(panel.getX());
+ viewer.setYpos(panel.getY());
+ viewer.setTitle(panel.getTitle());
+ PCAModel pcaModel = panel.getPcaModel();
+ viewer.setScoreModelName(pcaModel.getScoreModelName());
+ viewer.setXDim(panel.getSelectedDimensionIndex(X));
+ viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+ viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+ viewer.setBgColour(
+ panel.getRotatableCanvas().getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+ float[] spMin = panel.getRotatableCanvas().getSeqMin();
+ SeqPointMin spmin = new SeqPointMin();
+ spmin.setXPos(spMin[0]);
+ spmin.setYPos(spMin[1]);
+ spmin.setZPos(spMin[2]);
+ viewer.setSeqPointMin(spmin);
+ float[] spMax = panel.getRotatableCanvas().getSeqMax();
+ SeqPointMax spmax = new SeqPointMax();
+ spmax.setXPos(spMax[0]);
+ spmax.setYPos(spMax[1]);
+ spmax.setZPos(spMax[2]);
+ viewer.setSeqPointMax(spmax);
+ viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+ viewer.setLinkToAllViews(
+ panel.getRotatableCanvas().isApplyToAllViews());
+ SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+ viewer.setIncludeGaps(sp.includeGaps());
+ viewer.setMatchGaps(sp.matchGaps());
+ viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+ viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+ /*
+ * sequence points on display
+ */
+ for (jalview.datamodel.SequencePoint spt : pcaModel
+ .getSequencePoints())
+ {
+ SequencePoint point = new SequencePoint();
+ point.setSequenceRef(seqHash(spt.getSequence()));
+ point.setXPos(spt.coord.x);
+ point.setYPos(spt.coord.y);
+ point.setZPos(spt.coord.z);
+ viewer.getSequencePoint().add(point);
+ }
+
+ /*
+ * (end points of) axes on display
+ */
+ for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
+ {
+
+ Axis axis = new Axis();
+ axis.setXPos(p.x);
+ axis.setYPos(p.y);
+ axis.setZPos(p.z);
+ viewer.getAxis().add(axis);
+ }
+
+ /*
+ * raw PCA data (note we are not restoring PCA inputs here -
+ * alignment view, score model, similarity parameters)
+ */
+ PcaDataType data = new PcaDataType();
+ viewer.setPcaData(data);
+ PCA pca = pcaModel.getPcaData();
+
+ DoubleMatrix pm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getPairwiseScores(), pm);
+ data.setPairwiseMatrix(pm);
+
+ DoubleMatrix tm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getTridiagonal(), tm);
+ data.setTridiagonalMatrix(tm);
+
+ DoubleMatrix eigenMatrix = new DoubleMatrix();
+ data.setEigenMatrix(eigenMatrix);
+ saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
+
+ object.getPcaViewer().add(viewer);
+ } catch (Throwable t)
+ {
+ Cache.log.error("Error saving PCA: " + t.getMessage());
+ }
+ }
+
+ /**
+ * Stores values from a matrix into an XML element, including (if present) the
+ * D or E vectors
+ *
+ * @param m
+ * @param xmlMatrix
+ * @see #loadDoubleMatrix(DoubleMatrix)
+ */
+ protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
+ {
+ xmlMatrix.setRows(m.height());
+ xmlMatrix.setColumns(m.width());
+ for (int i = 0; i < m.height(); i++)
+ {
+ DoubleVector row = new DoubleVector();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.getV().add(m.getValue(i, j));
+ }
+ xmlMatrix.getRow().add(row);
+ }
+ if (m.getD() != null)
+ {
+ DoubleVector dVector = new DoubleVector();
+ for (double d : m.getD())
+ {
+ dVector.getV().add(d);
+ }
+ xmlMatrix.setD(dVector);
+ }
+ if (m.getE() != null)
+ {
+ DoubleVector eVector = new DoubleVector();
+ for (double e : m.getE())
+ {
+ eVector.getV().add(e);
+ }
+ xmlMatrix.setE(eVector);
+ }
+ }
+
+ /**
+ * Loads XML matrix data into a new Matrix object, including the D and/or E
+ * vectors (if present)
+ *
+ * @param mData
+ * @return
+ * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
+ */
+ protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
+ {
+ int rows = mData.getRows();
+ double[][] vals = new double[rows][];
+
+ for (int i = 0; i < rows; i++)
+ {
+ List<Double> dVector = mData.getRow().get(i).getV();
+ vals[i] = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vals[i][dvi++] = d;
+ }
+ }
+
+ MatrixI m = new Matrix(vals);
+
+ if (mData.getD() != null)
+ {
+ List<Double> dVector = mData.getD().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setD(vec);
+ }
+ if (mData.getE() != null)
+ {
+ List<Double> dVector = mData.getE().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setE(vec);
+ }
+
+ return m;
+ }
/**
* Save any Varna viewers linked to this sequence. Writes an rnaViewer element
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
- if (Desktop.desktop == null)
+ if (Desktop.getDesktopPane() == null)
{
return;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
if (frames[f] instanceof AppVarna)
{
if (jout != null)
{
+ jarEntryName = jarEntryName.replace('\\','/');
System.out.println("Writing jar entry " + jarEntryName);
jout.putNextEntry(new JarEntry(jarEntryName));
DataOutputStream dout = new DataOutputStream(jout);
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
- "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
}
// record the
// file so we
if (calcIdParam.getVersion().equals("1.0"))
{
final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ ServiceWithParameters service = PreferredServiceRegistry.getRegistry()
.getPreferredServiceFor(calcIds);
if (service != null)
{
argList = parmSet.getArguments();
parmSet = null;
}
- AAConSettings settings = new AAConSettings(
+ AutoCalcSetting settings = new AAConSettings(
calcIdParam.isAutoUpdate(), service, parmSet, argList);
av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
calcIdParam.isNeedsUpdate());
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a server in the Web Services preferences tab.");
return false;
}
}
vamsasSeq.setName(jds.getName());
vamsasSeq.setSequence(jds.getSequenceAsString());
vamsasSeq.setDescription(jds.getDescription());
- jalview.datamodel.DBRefEntry[] dbrefs = null;
+ List<DBRefEntry> dbrefs = null;
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
parentseq = jds;
}
}
+
+ /*
+ * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+ */
if (dbrefs != null)
{
- for (int d = 0; d < dbrefs.length; d++)
+ for (int d = 0, nd = dbrefs.size(); d < nd; d++)
{
DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
+ DBRefEntry ref = dbrefs.get(d);
+ dbref.setSource(ref.getSource());
+ dbref.setVersion(ref.getVersion());
+ dbref.setAccessionId(ref.getAccessionId());
+ if (ref instanceof GeneLocus)
{
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ dbref.setLocus(true);
+ }
+ if (ref.hasMap())
+ {
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
- // vamsasSeq.addDBRef(dbref);
vamsasSeq.getDBRef().add(dbref);
}
}
}
/**
- * contains last error message (if any) encountered by XML loader.
- */
- String errorMessage = null;
-
- /**
- * flag to control whether the Jalview2XML_V1 parser should be deferred to if
- * exceptions are raised during project XML parsing
- */
- public boolean attemptversion1parse = false;
-
- /**
* Load a jalview project archive from a jar file
*
* @param file
* - HTTP URL or filename
*/
- public AlignFrame loadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final Object file)
{
jalview.gui.AlignFrame af = null;
{
try
{
- SwingUtilities.invokeAndWait(new Runnable()
+// was invokeAndWait
+
+ // BH 2019 -- can't wait
+ SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
setLoadingFinishedForNewStructureViewers();
- };
+ }
});
} catch (Exception x)
{
System.err.println("Error loading alignment: " + x.getMessage());
}
}
+ this.jarFile = null;
return af;
}
+ @SuppressWarnings("unused")
private jarInputStreamProvider createjarInputStreamProvider(
- final String file) throws MalformedURLException
+ final Object ofile) throws MalformedURLException
{
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider()
+ try
{
+ String file = (ofile instanceof File
+ ? ((File) ofile).getCanonicalPath()
+ : ofile.toString());
+ byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+ : null;
+ if (bytes != null)
+ {
+ this.jarFile = (File) ofile;
+ }
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
- @Override
- public JarInputStream getJarInputStream() throws IOException
+ URL url = file.startsWith("http://") ? new URL(file) : null;
+ return new jarInputStreamProvider()
{
- if (_url != null)
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
{
- return new JarInputStream(_url.openStream());
+ InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+ : (url != null ? url.openStream()
+ : new FileInputStream(file));
+ return new JarInputStream(is);
}
- else
+
+ @Override
+ public File getFile()
{
- return new JarInputStream(new FileInputStream(file));
+ return jarFile;
}
- }
- @Override
- public String getFilename()
- {
- return file;
- }
- };
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ return null;
+ }
}
/**
AlignFrame af = null, _af = null;
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
- final String file = jprovider.getFilename();
+ String fileName = jprovider.getFilename();
+ File file = jprovider.getFile();
+ List<AlignFrame> alignFrames = new ArrayList<>();
+
try
{
JarInputStream jin = null;
JarEntry jarentry = null;
int entryCount = 1;
+
+ // Look for all the entry names ending with ".xml"
+ // This includes all panels and at least one frame.
+// Platform.timeCheck(null, Platform.TIME_MARK);
do
{
jin = jprovider.getJarInputStream();
{
jarentry = jin.getNextJarEntry();
}
+ String name = (jarentry == null ? null : jarentry.getName());
- if (jarentry != null && jarentry.getName().endsWith(".xml"))
+// System.out.println("Jalview2XML opening " + name);
+ if (name != null && name.endsWith(".xml"))
{
- InputStreamReader in = new InputStreamReader(jin, UTF_8);
- // JalviewModel object = new JalviewModel();
+ // DataSet for.... is read last.
+
+
+ // The question here is what to do with the two
+ // .xml files in the jvp file.
+ // Some number of them, "...Dataset for...", will be the
+ // Only AlignPanels and will have Viewport.
+ // One or more will be the source data, with the DBRefs.
+ //
+ // JVP file writing (above) ensures tha the AlignPanels are written
+ // first, then all relevant datasets (which are
+ // Jalview.datamodel.Alignment).
+ //
+
+// Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
JAXBElement<JalviewModel> jbe = um
.unmarshal(streamReader, JalviewModel.class);
- JalviewModel object = jbe.getValue();
+ JalviewModel model = 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.getViewport().size() > 0)
- // getJalviewModelSequence().getViewportCount() > 0)
+ // Q: Do we have to load from the model, even if it
+ // does not have a viewport, could we discover that early on?
+ // Q: Do we need to load this object?
+ _af = loadFromObject(model, fileName, file, true, jprovider);
+// Platform.timeCheck("Jalview2XML.loadFromObject",
+ // Platform.TIME_MARK);
+
+ if (_af != null)
{
+ alignFrames.add(_af);
+ }
+ if (_af != null && model.getViewport().size() > 0)
+ {
+
+ // That is, this is one of the AlignmentPanel models
if (af == null)
{
// store a reference to the first view
} catch (IOException ex)
{
ex.printStackTrace();
- errorMessage = "Couldn't locate Jalview XML file : " + file;
+ errorMessage = "Couldn't locate Jalview XML file : " + fileName;
System.err.println(
"Exception whilst loading jalview XML file : " + ex + "\n");
} catch (Exception ex)
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)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
if (af != null)
{
errorMessage = "Out of memory loading jalview XML file";
System.err.println("Out of memory whilst loading jalview XML file");
e.printStackTrace();
+ } finally
+ {
+ for (AlignFrame alf : alignFrames)
+ {
+ alf.alignPanel.setHoldRepaint(false);
+ }
+
}
/*
*/
for (AlignFrame fr : gatherToThisFrame.values())
{
- Desktop.instance.gatherViews(fr);
+ Desktop.getInstance().gatherViews(fr);
}
restoreSplitFrames();
{
if (ds.getCodonFrames() != null)
{
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerMappings(ds.getCodonFrames());
}
}
reportErrors();
}
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
return af;
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");
*/
for (SplitFrame sf : gatherTo)
{
- Desktop.instance.gatherViews(sf);
+ Desktop.getInstance().gatherViews(sf);
}
splitFrameCandidates.clear();
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
finalErrorMessage,
"Error " + (saving ? "saving" : "loading")
+ " Jalview file",
}
/**
- * Load alignment frame from jalview XML DOM object
+ * Load alignment frame from jalview XML DOM object. For a DOM object that
+ * includes one or more Viewport elements (one with a title that does NOT
+ * contain "Dataset for"), create the frame.
*
* @param jalviewModel
* DOM
- * @param file
+ * @param fileName
* filename source string
+ * @param file
* @param loadTreesAndStructures
* when false only create Viewport
* @param jprovider
* data source provider
* @return alignment frame created from view stored in DOM
*/
- AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
- boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
+ AlignFrame loadFromObject(JalviewModel jalviewModel, String fileName,
+ File file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
+
// JalviewModelSequence jms = object.getJalviewModelSequence();
// Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
: null;
// ////////////////////////////////
+ // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
+ //
+ //
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
+
+ /**
+ * used to resolve correct alignment dataset for alignments with multiple
+ * views
+ */
+ String uniqueSeqSetId = null;
+ String viewId = null;
+ if (view != null)
+ {
+ uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+ viewId = (view.getId() == null ? null
+ : view.getId() + uniqueSetSuffix);
+ }
+
+ // ////////////////////////////////
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
|| tmpSeq.getEnd() != jseq.getEnd())
{
System.err.println(
- "Warning JAL-2154 regression: updating start/end for sequence "
- + tmpSeq.toString() + " to " + jseq);
+ String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+ tmpSeq.getName(), tmpSeq.getStart(),
+ tmpSeq.getEnd(), jseq.getStart(),
+ jseq.getEnd()));
}
}
else
vi++;
}
- if (jseq.isViewreference() != null
- && jseq.isViewreference().booleanValue())
+ if (safeBoolean(jseq.isViewreference()))
{
referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
}
// finally, verify all data in vamsasSet is actually present in al
// passing on flag indicating if it is actually a stored dataset
- recoverDatasetFor(vamsasSet, al, isdsal);
+ recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
}
if (referenceseqForView != null)
Feature feat = features.get(f);
SequenceFeature sf = new SequenceFeature(feat.getType(),
feat.getDescription(), feat.getBegin(), feat.getEnd(),
- feat.getScore(), feat.getFeatureGroup());
+ safeFloat(feat.getScore()), feat.getFeatureGroup());
sf.setStatus(feat.getStatus());
/*
{
entry.setProperty(prop.getName(), prop.getValue());
}
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
}
}
}
+
+ /*
+ * load any HMMER profile
+ */
+ // TODO fix this
+
+ String hmmJarFile = jseqs.get(i).getHmmerProfile();
+ if (hmmJarFile != null && jprovider != null)
+ {
+ loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
+ }
}
} // end !multipleview
// 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.isVisible() != null) // annotation.hasVisible())
+ if (annotation.isVisible() != null)
{
jda.visible = annotation.isVisible();
}
continue;
}
- float value = annElement.getValue() == null ? 0f
- : annElement.getValue().floatValue();
+ float value = safeFloat(annElement.getValue());
anot[anpos] = new jalview.datamodel.Annotation(
annElement.getDisplayCharacter(),
annElement.getDescription(),
.getSecondaryStructure()
.charAt(0),
value);
- // JBPNote: Consider verifying dataflow for IO of secondary
- // structure annotation read from Stockholm files
- // this was added to try to ensure that
- // if (anot[ annElement.getPosition()].secondaryStructure>' ')
- // {
- // anot[ annElement.getPosition()].displayCharacter = "";
- // }
- final int colourValue = annElement.getColour() == null ? 0
- : annElement.getColour().intValue();
- anot[anpos].colour = new java.awt.Color(colourValue);
+ anot[anpos].colour = new Color(safeInt(annElement.getColour()));
if (firstColour == null)
{
firstColour = anot[anpos].colour;
}
}
}
+ // create the new AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation jaa = null;
if (annotation.isGraph())
// }
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())
{
jaa._linecolour = firstColour;
}
// register new annotation
+ // Annotation graphs such as Conservation will not have id.
if (annotation.getId() != null)
{
annotationIds.put(annotation.getId(), jaa);
if (annotation.getScore() != null)
{
- jaa.setScore(annotation.getScore());
+ jaa.setScore(annotation.getScore().doubleValue());
}
if (annotation.isVisible() != null)
{
{
jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
}
- if (/*annotation.hasAutoCalculated() && */annotation
- .isAutoCalculated())
+ if (annotation.isAutoCalculated())
{
// newer files have an 'autoCalculated' flag and store calculation
// state in viewport properties
{
jaa.graphHeight = annotation.getGraphHeight().intValue();
}
- // if (annotation.hasBelowAlignment())
- // {
- // schema specifies default for optional attribute
- jaa.belowAlignment = annotation.isBelowAlignment();
- // }
+ jaa.belowAlignment = annotation.isBelowAlignment();
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
- int pidThreshold = jGroup.getPidThreshold() == null ? 0
- : jGroup.getPidThreshold().intValue();
+ int pidThreshold = safeInt(jGroup.getPidThreshold());
Vector<SequenceI> seqs = new Vector<>();
}
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
- jGroup.isDisplayBoxes(), jGroup.isDisplayText(),
- jGroup.isColourText(), 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() == null ? 0
- : jGroup.getConsThreshold().intValue());
- sg.setOutlineColour(
- new java.awt.Color(jGroup.getOutlineColour() == null ? 0
- : jGroup.getOutlineColour().intValue()));
-
- sg.textColour = new java.awt.Color(jGroup.getTextCol1());
- sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
- sg.setShowNonconserved(
- jGroup.isShowUnconserved() != null
- ? jGroup.isShowUnconserved().booleanValue()
- : false);
- sg.thresholdTextColour = jGroup.getTextColThreshold();
+ .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
- // if (jGroup.hasShowConsensusHistogram())
- // {
sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- // }
- // if (jGroup.hasShowSequenceLogo())
- // {
sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- // }
- // if (jGroup.hasNormaliseSequenceLogo())
- // {
sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
- // }
- // if (jGroup.hasIgnoreGapsinConsensus())
- // {
sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
- // }
if (jGroup.getConsThreshold() != null
&& jGroup.getConsThreshold().intValue() != 0)
{
// ///////////////////////////////
// LOAD VIEWPORT
- // If we just load in the same jar file again, the sequenceSetId
- // will be the same, and we end up with multiple references
- // to the same sequenceSet. We must modify this id on load
- // so that each load of the file gives a unique id
- String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- String viewId = (view.getId() == null ? null
- : view.getId() + uniqueSetSuffix);
- AlignFrame af = null;
- AlignViewport av = null;
// now check to see if we really need to create a new viewport.
if (multipleView && viewportsAdded.size() == 0)
{
boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
jalviewModel.getVersion());
+ AlignFrame af = null;
AlignmentPanel ap = null;
- boolean isnewview = true;
+ AlignViewport av = null;
if (viewId != null)
{
// Check to see if this alignment already has a view id == viewId
{
for (int v = 0; v < views.length; v++)
{
- if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ ap = views[v];
+ av = ap.av;
+ if (av.getViewId().equalsIgnoreCase(viewId))
{
// recover the existing alignpanel, alignframe, viewport
- af = views[v].alignFrame;
- av = views[v].av;
- ap = views[v];
+ af = ap.alignFrame;
+ break;
// TODO: could even skip resetting view settings if we don't want to
// change the local settings from other jalview processes
- isnewview = false;
}
}
}
}
- if (isnewview)
+ if (af == null)
{
- af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
+ af = loadViewport(fileName, file, jseqs, hiddenSeqs, al, jalviewModel, view,
uniqueSeqSetId, viewId, autoAlan);
av = af.getViewport();
+ // note that this only retrieves the most recently accessed
+ // tab of an AlignFrame.
ap = af.alignPanel;
}
*
* Not done if flag is false (when this method is used for New View)
*/
+ final AlignFrame af0 = af;
+ final AlignViewport av0 = av;
+ final AlignmentPanel ap0 = ap;
+// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
+// Platform.TIME_MARK);
if (loadTreesAndStructures)
{
- loadTrees(jalviewModel, view, af, av, ap);
- loadPDBStructures(jprovider, jseqs, af, ap);
- loadRnaViewers(jprovider, jseqs, ap);
+ if (!jalviewModel.getTree().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+// Platform.timeCheck(null, Platform.TIME_MARK);
+ loadTrees(jalviewModel, view, af0, av0, ap0);
+// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
+ }
+ });
+ }
+ if (!jalviewModel.getPcaViewer().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+// Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPCAViewers(jalviewModel, ap0);
+// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
+ }
+ });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+// Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPDBStructures(jprovider, jseqs, af0, ap0);
+// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
+ }
+ });
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ loadRnaViewers(jprovider, jseqs, ap0);
+ }
+ });
}
// and finally return.
+ // but do not set holdRepaint true just yet, because this could be the
+ // initial frame with just its dataset.
return af;
}
/**
+ * Loads a HMMER profile from a file stored in the project, and associates it
+ * with the specified sequence
+ *
+ * @param jprovider
+ * @param hmmJarFile
+ * @param seq
+ */
+ protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+ String hmmJarFile, SequenceI seq)
+ {
+ try
+ {
+ String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+ HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+ HiddenMarkovModel hmmModel = parser.getHMM();
+ hmmModel = new HiddenMarkovModel(hmmModel, seq);
+ seq.setHMM(hmmModel);
+ } catch (IOException e)
+ {
+ warn("Error loading HMM profile for " + seq.getName() + ": "
+ + e.getMessage());
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
* @param jseqs
* @param ap
*/
- private void loadRnaViewers(jarInputStreamProvider jprovider,
+ protected void loadRnaViewers(jarInputStreamProvider jprovider,
List<JSeq> jseqs, AlignmentPanel ap)
{
/*
* 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,
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
- appVarna.setInitialSelection(viewer.getSelectedRna());
+ appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
}
}
}
* 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;
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 (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
if (tree.getId() != null)
{
// perhaps bind the tree id to something ?
// 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.setViewport(av); // af.viewport; // TODO: verify 'associate with all
- // views'
- // works still
+ 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)
- {
- warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
- continue;
}
-
- tp.fitToWindow.setState(tree.isFitToWindow());
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
+ 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.isMarkUnlinked());
- tp.showBootstrap(tree.isShowBootstrap());
- tp.showDistances(tree.isShowDistances());
+ tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
+ tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
+ tp.showDistances(safeBoolean(tree.isShowDistances()));
- tp.getTreeCanvas().setThreshold(tree.getThreshold());
+ tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
- if (tree.isCurrentTree())
+ if (safeBoolean(tree.isCurrentTree()))
{
af.getViewport().setCurrentTree(tp.getTree());
}
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);
+ // Desktop.getDesktop().getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
pdbid.getFile());
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera", null);
+ "chimera", ".py");
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ newFileLoc
+ .append(Platform.escapeBackslashes(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
final AlignFrame alf = af;
final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
svattrib.getWidth(), svattrib.getHeight());
- try
- {
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+
+ // BH again was invokeAndWait
+ // try
+ // {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
}
}
});
- } catch (InvocationTargetException ex)
- {
- warn("Unexpected error when opening Jmol view.", ex);
-
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
+ // } catch (InvocationTargetException ex)
+ // {
+ // warn("Unexpected error when opening Jmol view.", ex);
+ //
+ // } catch (InterruptedException e)
+ // {
+ // // e.printStackTrace();
+ // }
}
{
try
{
- frames = Desktop.desktop.getAllFrames();
+ frames = Desktop.getDesktopPane().getAllFrames();
} catch (ArrayIndexOutOfBoundsException e)
{
// occasional No such child exceptions are thrown here...
}
}
- AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ AlignFrame loadViewport(String fileName, File file, List<JSeq> JSEQ,
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
- af = new AlignFrame(al, view.getWidth(), view.getHeight(),
- uniqueSeqSetId, viewId);
-
- af.setFileName(file, FileFormat.Jalview);
+ af = new AlignFrame(al, safeInt(view.getWidth()),
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+ // {
+ //
+ // @Override
+ // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+ // System.out.println("Jalview2XML AF " + e);
+ // super.processKeyEvent(e);
+ //
+ // }
+ //
+ // }
+ ;
+ af.alignPanel.setHoldRepaint(true);
+ af.setFile(fileName, file, null, FileFormat.Jalview);
+ af.setFileObject(jarFile); // BH 2019 JAL-3436
final AlignViewport viewport = af.getViewport();
for (int i = 0; i < JSEQ.size(); i++)
{
- viewport.setSequenceColour(
- viewport.getAlignment().getSequenceAt(i),
- new java.awt.Color(JSEQ.get(i).getColour()));
+ int colour = safeInt(JSEQ.get(i).getColour());
+ viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i),
+ new Color(colour));
}
if (al.hasSeqrep())
viewport.setDisplayReferenceSeq(true);
}
- viewport.setGatherViewsHere(view.isGatheredViews());
+ viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews()));
if (view.getSequenceSetId() != null)
{
}
// recover view properties and display parameters
- viewport.setShowAnnotation(view.isShowAnnotation());
- viewport.setAbovePIDThreshold(view.isPidSelected());
- final int pidThreshold = view.getPidThreshold() == null ? 0
- : view.getPidThreshold().intValue();
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
+ viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
+ final int pidThreshold = safeInt(view.getPidThreshold());
viewport.setThreshold(pidThreshold);
- viewport.setColourText(view.isShowColourText());
+ viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(view.isConservationSelected());
- viewport.setIncrement(view.getConsThreshold() == null ? 0
- : view.getConsThreshold().intValue());
- viewport.setShowJVSuffix(view.isShowFullId());
- viewport.setRightAlignIds(view.isRightAlignIds());
- viewport.setFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(), view.getFontSize()), true);
+ 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());
viewport.setViewStyle(vs);
// TODO: allow custom charWidth/Heights to be restored by updating them
// after setting font - which means set above to false
- viewport.setRenderGaps(view.isRenderGaps());
- viewport.setWrapAlignment(view.isWrapAlignment());
- viewport.setShowAnnotation(view.isShowAnnotation());
+ viewport.setRenderGaps(safeBoolean(view.isRenderGaps()));
+ viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
+ viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
- viewport.setShowBoxes(view.isShowBoxes());
+ viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
- viewport.setShowText(view.isShowText());
+ viewport.setShowText(safeBoolean(view.isShowText()));
- viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
- viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
- viewport.setThresholdTextColour(view.getTextColThreshold());
- viewport.setShowUnconserved(
- view.isShowUnconserved() ? view.isShowUnconserved() : false);
- 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)
{
viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
+ int x = safeInt(view.getXpos());
+ int y = safeInt(view.getYpos());
+ int w = safeInt(view.getWidth());
+ int h = safeInt(view.getHeight());
+ // // BH we cannot let the title bar go off the top
+ // if (Platform.isJS())
+ // {
+ // x = Math.max(50 - w, x);
+ // y = Math.max(0, y);
+ // }
+
+ af.setBounds(x, y, w, h);
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+ view.getBgColour());
}
}
+ /*
+ * turn off 'alignment colour applies to all groups'
+ * while restoring global colour scheme
+ */
+ viewport.setColourAppliesToAllGroups(false);
viewport.setGlobalColourScheme(cs);
viewport.getResidueShading().setThreshold(pidThreshold,
view.isIgnoreGapsinConsensus());
viewport.getResidueShading()
.setConsensus(viewport.getSequenceConsensusHash());
- viewport.setColourAppliesToAllGroups(false);
-
- if (view.isConservationSelected() && cs != null)
+ if (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
- .setConservationInc(view.getConsThreshold());
+ .setConservationInc(safeInt(view.getConsThreshold()));
}
-
af.changeColour(cs);
-
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(view.isShowSequenceFeatures());
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
- // if (view.hasCentreColumnLabels())
- // {
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
- // }
- // if (view.hasIgnoreGapsinConsensus())
- // {
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
- // }
- // if (view.hasFollowHighlight())
- // {
-
viewport.setFollowHighlight(view.isFollowHighlight());
- // }
- // if (view.hasFollowSelection())
- // {
viewport.followSelection = view.isFollowSelection();
- // }
- // if (view.hasShowConsensusHistogram())
- // {
viewport.setShowConsensusHistogram(view.isShowConsensusHistogram());
- // }
- // else
- // {
- // viewport.setShowConsensusHistogram(true);
- // }
- // if (view.hasShowSequenceLogo())
- // {
viewport.setShowSequenceLogo(view.isShowSequenceLogo());
- // }
- // else
- // {
- // viewport.setShowSequenceLogo(false);
- // }
- // if (view.hasNormaliseSequenceLogo())
- // {
viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo());
- // }
- if (view.isShowDbRefTooltip() != null)
- {
- viewport.setShowDBRefs(view.isShowDbRefTooltip());
- }
- if (view.isShowNPfeatureTooltip() != null)
- {
- viewport.setShowNPFeats(view.isShowNPfeatureTooltip());
- }
- // if (view.hasShowGroupConsensus())
- // {
+ viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip()));
+ viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
viewport.setShowGroupConsensus(view.isShowGroupConsensus());
- // }
- // else
- // {
- // viewport.setShowGroupConsensus(false);
- // }
- // if (view.hasShowGroupConservation())
- // {
viewport.setShowGroupConservation(view.isShowGroupConservation());
- // }
- // else
- // {
- // viewport.setShowGroupConservation(false);
- // }
+ viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+ viewport.setShowComplementFeaturesOnTop(
+ view.isShowComplementFeaturesOnTop());
// recover feature settings
if (jm.getFeatureSettings() != null)
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .unmarshalFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
{
noValueColour = maxColour;
}
- float min = setting.getMin() != null
- ? setting.getMin().floatValue()
- : 0f;
- float max = setting.getMin() != null
- ? setting.getMax().floatValue()
- : 1f;
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
- noValueColour, min, max);
+ float min = safeFloat(safeFloat(setting.getMin()));
+ float max = setting.getMax() == null ? 1f
+ : setting.getMax().floatValue();
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
if (setting.getThreshold() != null)
{
gc.setThreshold(setting.getThreshold().floatValue());
- int threshstate = setting.getThreshstate().intValue();
+ int threshstate = safeInt(setting.getThreshstate());
// -1 = None, 0 = Below, 1 = Above threshold
if (threshstate == 0)
{
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
}
else
{
- featureOrder.put(featureType, new Float(
+ featureOrder.put(featureType, Float.valueOf(
fs / jm.getFeatureSettings().getSetting().size()));
}
- if (setting.isDisplay())
+ if (safeBoolean(setting.isDisplay()))
{
fdi.setVisible(featureType);
}
for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
{
Group grp = jm.getFeatureSettings().getGroup().get(gs);
- fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+ fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
}
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
{
for (int c = 0; c < view.getHiddenColumns().size(); c++)
{
- viewport.hideColumns(view.getHiddenColumns().get(c).getStart(),
- view.getHiddenColumns().get(c).getEnd() // +1
- );
+ final HiddenColumns hc = view.getHiddenColumns().get(c);
+ viewport.hideColumns(safeInt(hc.getStart()),
+ safeInt(hc.getEnd()) /* +1 */);
}
}
if (view.getCalcIdParam() != null)
String complementaryViewId = view.getComplementId();
if (complementaryViewId == null)
{
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
- view.getHeight());
+ Dimension dim = Platform.getDimIfEmbedded(af,
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
+ Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
}
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(model, viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
+ safeInt(viewAnnColour.getAboveThreshold()));
}
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), 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);
AnnotationColourGradient groupScheme = new AnnotationColourGradient(
matchedAnnotation, sg.getColourScheme(),
- viewAnnColour.getAboveThreshold());
+ safeInt(viewAnnColour.getAboveThreshold()));
sg.setColourScheme(groupScheme);
groupScheme.setSeqAssociated(perSequenceOnly);
groupScheme.setPredefinedColours(useOriginalColours);
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
return true;
}
return false;
}
- public void addToSkipList(AlignFrame af)
+ protected void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
skipList.put(af.getViewport().getSequenceSetId(), af);
}
- public void clearSkipList()
+ protected void clearSkipList()
{
if (skipList != null)
{
}
private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
- boolean ignoreUnrefed)
+ boolean ignoreUnrefed, String uniqueSeqSetId)
{
jalview.datamodel.AlignmentI ds = getDatasetFor(
vamsasSet.getDatasetId());
+ AlignmentI xtant_ds = ds;
+ if (xtant_ds == null)
+ {
+ // good chance we are about to create a new dataset, but check if we've
+ // seen some of the dataset sequence IDs before.
+ // TODO: skip this check if we are working with project generated by
+ // version 2.11 or later
+ xtant_ds = checkIfHasDataset(vamsasSet.getSequence());
+ if (xtant_ds != null)
+ {
+ ds = xtant_ds;
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ }
Vector dseqs = null;
+ if (!ignoreUnrefed)
+ {
+ // recovering an alignment View
+ AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
+ if (seqSetDS != null)
+ {
+ if (ds != null && ds != seqSetDS)
+ {
+ warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ + " - CDS/Protein crossreference data may be lost");
+ if (xtant_ds != null)
+ {
+ // This can only happen if the unique sequence set ID was bound to a
+ // dataset that did not contain any of the sequences in the view
+ // currently being restored.
+ warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ }
+ }
+ ds = seqSetDS;
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ }
if (ds == null)
{
+ // try even harder to restore dataset
+ AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
// create a list of new dataset sequences
dseqs = new Vector();
}
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset " + vamsasSet.getDatasetId()
- + " for alignment " + System.identityHashCode(al));
+// debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
+// + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
+ // register dataset for the alignment's uniqueSeqSetId for legacy projects
+ addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds);
}
+ updateSeqDatasetBinding(vamsasSet.getSequence(), ds);
}
/**
+ * XML dataset sequence ID to materialised dataset reference
+ */
+ HashMap<String, AlignmentI> seqToDataset = new HashMap<>();
+
+ /**
+ * @return the first materialised dataset reference containing a dataset
+ * sequence referenced in the given view
+ * @param list
+ * - sequences from the view
+ */
+ AlignmentI checkIfHasDataset(List<Sequence> list)
+ {
+ for (Sequence restoredSeq : list)
+ {
+ AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid());
+ if (datasetFor != null)
+ {
+ return datasetFor;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Register ds as the containing dataset for the dataset sequences referenced
+ * by sequences in list
+ *
+ * @param list
+ * - sequences in a view
+ * @param ds
+ */
+ void updateSeqDatasetBinding(List<Sequence> list, AlignmentI ds)
+ {
+ for (Sequence restoredSeq : list)
+ {
+ AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
+ if (prevDS != null && prevDS != ds)
+ {
+ warn("Dataset sequence appears in many datasets: "
+ + restoredSeq.getDsseqid());
+ // TODO: try to merge!
+ }
+ }
+ }
+ /**
*
* @param vamsasSeq
* sequence definition to create/merge dataset sequence for
return datasetId;
}
+ /**
+ * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+ * constructed as a special subclass GeneLocus.
+ *
+ * @param datasetSequence
+ * @param sequence
+ */
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRef().size(); d++)
{
DBRef dr = sequence.getDBRef().get(d);
- jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- dr.getSource(), dr.getVersion(), dr.getAccessionId());
+ DBRefEntry entry;
+ if (dr.isLocus())
+ {
+ entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
+ else
+ {
+ entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
fto, m.getMapFromUnit().intValue(),
m.getMapToUnit().intValue());
- // if (m.getMappingChoice() != null)
- // {
- // MappingChoice mc = m.getMappingChoice();
+
+ /*
+ * (optional) choice of dseqFor or Sequence
+ */
if (m.getDseqFor() != null)
{
String dsfor = m.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
- /**
+ /*
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
- else
+ else if (m.getSequence() != null)
{
- /**
+ /*
* local sequence definition
*/
Sequence ms = m.getSequence();
jmap.setTo(djs);
incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
-
}
jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
initSeqRefs();
JalviewModel jm = saveState(ap, null, null, null);
+ addDatasetRef(
+ jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
+ ap.getAlignment().getDataset());
+
uniqueSetSuffix = "";
// jm.getJalviewModelSequence().getViewport(0).setId(null);
jm.getViewport().get(0).setId(null);
viewportsAdded.clear();
- AlignFrame af = loadFromObject(jm, null, false, null);
+ AlignFrame af = loadFromObject(jm, null, null, false, null);
af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
+ af.alignPanel.setHoldRepaint(false);
+ this.jarFile = null;
/*
* if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
/**
+ * Loads any saved PCA viewers
+ *
+ * @param jms
+ * @param ap
+ */
+ protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
+ {
+ try
+ {
+ List<PcaViewer> pcaviewers = model.getPcaViewer();
+ for (PcaViewer viewer : pcaviewers)
+ {
+ String modelName = viewer.getScoreModelName();
+ SimilarityParamsI params = new SimilarityParams(
+ viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
+ viewer.isIncludeGaps(),
+ viewer.isDenominateByShortestLength());
+
+ /*
+ * create the panel (without computing the PCA)
+ */
+ PCAPanel panel = new PCAPanel(ap, modelName, params);
+
+ panel.setTitle(viewer.getTitle());
+ panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
+ viewer.getWidth(), viewer.getHeight()));
+
+ boolean showLabels = viewer.isShowLabels();
+ panel.setShowLabels(showLabels);
+ panel.getRotatableCanvas().setShowLabels(showLabels);
+ panel.getRotatableCanvas()
+ .setBgColour(new Color(viewer.getBgColour()));
+ panel.getRotatableCanvas()
+ .setApplyToAllViews(viewer.isLinkToAllViews());
+
+ /*
+ * load PCA output data
+ */
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ PCA pca = new PCA(null, scoreModel, params);
+ PcaDataType pcaData = viewer.getPcaData();
+
+ MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
+ pca.setPairwiseScores(pairwise);
+
+ MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
+ pca.setTridiagonal(triDiag);
+
+ MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
+ pca.setEigenmatrix(result);
+
+ panel.getPcaModel().setPCA(pca);
+
+ /*
+ * we haven't saved the input data! (JAL-2647 to do)
+ */
+ panel.setInputData(null);
+
+ /*
+ * add the sequence points for the PCA display
+ */
+ List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+ for (SequencePoint sp : viewer.getSequencePoint())
+ {
+ String seqId = sp.getSequenceRef();
+ SequenceI seq = seqRefIds.get(seqId);
+ if (seq == null)
+ {
+ throw new IllegalStateException(
+ "Unmatched seqref for PCA: " + seqId);
+ }
+ Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+ jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+ seq, pt);
+ seqPoints.add(seqPoint);
+ }
+ panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
+
+ /*
+ * set min-max ranges and scale after setPoints (which recomputes them)
+ */
+ panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
+ SeqPointMin spMin = viewer.getSeqPointMin();
+ float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+ spMin.getZPos() };
+ SeqPointMax spMax = viewer.getSeqPointMax();
+ float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+ spMax.getZPos() };
+ panel.getRotatableCanvas().setSeqMinMax(min, max);
+
+ // todo: hold points list in PCAModel only
+ panel.getPcaModel().setSequencePoints(seqPoints);
+
+ panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+ panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+ panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+ // is this duplication needed?
+ panel.setTop(seqPoints.size() - 1);
+ panel.getPcaModel().setTop(seqPoints.size() - 1);
+
+ /*
+ * add the axes' end points for the display
+ */
+ for (int i = 0; i < 3; i++)
+ {
+ Axis axis = viewer.getAxis().get(i);
+ panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
+ axis.getXPos(), axis.getYPos(), axis.getZPos());
+ }
+
+ Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), dim.width,
+ dim.height);
+ }
+ } catch (Exception ex)
+ {
+ Cache.log.error("Error loading PCA: " + ex.toString());
+ }
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
* @param fcol
* @return
*/
- protected static Colour marshalColour(
+ public static Colour marshalColour(
String featureType, FeatureColourI fcol)
{
Colour col = new Colour();
* @param and
* if true, conditions are and-ed, else or-ed
*/
- protected static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
+ public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
boolean and)
{
* @param matcherSetModel
* @return
*/
- protected static FeatureMatcherSetI unmarshalFilter(
+ 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
* @throws IllegalStateException
* if AND and OR conditions are mixed
*/
- protected static void unmarshalFilterConditions(
+ protected static void parseFilterConditions(
FeatureMatcherSetI matcherSet,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
boolean and)
* compound condition
*/
List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
- .getCompoundMatcher()
- .getMatcherSet();
+ .getCompoundMatcher().getMatcherSet();
boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
if (matchers.size() == 2)
{
- unmarshalFilterConditions(matcherSet, matchers.get(0), anded);
- unmarshalFilterConditions(matcherSet, matchers.get(1), anded);
+ parseFilterConditions(matcherSet, matchers.get(0), anded);
+ parseFilterConditions(matcherSet, matchers.get(1), anded);
}
else
{
* @param colourModel
* @return
*/
- protected static FeatureColourI unmarshalColour(Colour colourModel)
+ public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
- colourModel.getMin(),
- colourModel.getMax());
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
+ safeFloat(colourModel.getMin()),
+ safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();
String[] attributes = attributeName
.toArray(new String[attributeName.size()]);
git://source.jalview.org / jalview.git / blobdiff