*/
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.AlignmentI;
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;
private Map<RnaModel, String> rnaSessions = new HashMap<>();
/**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the boolean value, or false
+ * if null.
+ *
+ * @param b
+ * @return
+ */
+ public static boolean safeBoolean(Boolean b)
+ {
+ return b == null ? false : b.booleanValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the integer value, or zero
+ * if null.
+ *
+ * @param i
+ * @return
+ */
+ public static int safeInt(Integer i)
+ {
+ return i == null ? 0 : i.intValue();
+ }
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the float value, or zero if
+ * null.
+ *
+ * @param f
+ * @return
+ */
+ public static float safeFloat(Float f)
+ {
+ return f == null ? 0f : f.floatValue();
+ }
+
+ /**
* create/return unique hash string for sq
*
* @param sq
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)
{
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");
: 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;
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());
/*
// 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;
// }
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())
{
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 (loadTreesAndStructures)
{
loadTrees(jalviewModel, view, af, av, ap);
+ loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, 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 (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;
+ // FIXME: should we use safeBoolean here ?
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
}
if (tp == null)
continue;
}
- tp.fitToWindow.setState(tree.isFitToWindow());
+ 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);
String viewId, List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
- af = new AlignFrame(al, view.getWidth(), view.getHeight(),
- uniqueSeqSetId, viewId);
+ af = new AlignFrame(al, safeInt(view.getWidth()),
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId);
af.setFileName(file, FileFormat.Jalview);
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);
+ .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());
+ af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
}
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());
+ .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);
- // }
// recover feature settings
if (jm.getFeatureSettings() != null)
if (filters != null)
{
FeatureMatcherSetI filter = Jalview2XML
- .unmarshalFilter(featureType, filters);
+ .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,
+ 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)
{
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)
{
featureOrder.put(featureType, new Float(
fs / jm.getFeatureSettings().getSetting().size()));
}
- if (setting.isDisplay())
+ if (safeBoolean(setting.isDisplay()))
{
fdi.setVisible(featureType);
}
{
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());
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
// 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);
}
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
* @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;
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