*/
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.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.DBRefEntry;
import jalview.datamodel.GraphLine;
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.NewickFile;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
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.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
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;
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;
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
{
try
{
- FileOutputStream fos = new FileOutputStream(jarFile);
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(jarFile);
+ FileOutputStream fos = new FileOutputStream(
+ backupfiles.getTempFilePath());
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
}
;
jout.close();
- return true;
+ boolean success = true;
+
+ 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";
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.desktop != null)
+ {
+ for (JInternalFrame frame : Desktop.desktop.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
}
/**
+ * 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
* for each viewer, with
* <ul>
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)
{
: 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;
// 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)
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
// ///////////////////////////////
// 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 (loadTreesAndStructures)
{
loadTrees(jalviewModel, view, af, av, ap);
+ loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
// TODO: verify 'associate with all views' works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
+ // FIXME: should we use safeBoolean here ?
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
}
if (tp == 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 (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
.setConservationInc(safeInt(view.getConsThreshold()));
}
-
af.changeColour(cs);
-
viewport.setColourAppliesToAllGroups(true);
viewport
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), al,
viewAnnColour.getColourScheme()),
safeInt(viewAnnColour.getAboveThreshold()));
}
}
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();
}
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
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();
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);
}
/**
+ * 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());
+ }
+
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), 475, 450);
+ }
+ } 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
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();
git://source.jalview.org / jalview.git / blobdiff