X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=13f66d973ffeaf84e2085f32bd7e07f85db678c4;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=eedc8637a906cbebedf5954e85bad31a334e463f;hpb=b76d0ffcb6effa94954f75e030d1d67c890134eb;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index eedc863..13f66d9 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -40,6 +40,7 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.StructureSelectionManagerProvider; import jalview.bin.*; @@ -48,14 +49,15 @@ import jalview.datamodel.*; import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport implements SelectionSource +public class AlignViewport implements SelectionSource, VamsasSource { private static final int RIGHT_JUSTIFY = 1; @@ -539,12 +541,14 @@ public class AlignViewport implements SelectionSource try { - int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null // pointer // possibility // here. - if (aWidth < 0) + if (aWidth <= 0) { + updatingConsensus = false; + UPDATING_CONSENSUS = false; return; } @@ -552,8 +556,8 @@ public class AlignViewport implements SelectionSource consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus, true); + AAFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hconsensus, true); updateAnnotation(true); if (globalColourScheme != null) @@ -589,7 +593,8 @@ public class AlignViewport implements SelectionSource protected void updateAnnotation(boolean immediate) { - // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished. + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. if (immediate || (!updatingConsensus && consensus != null && hconsensus != null)) { @@ -639,9 +644,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return null or the currently selected sequence region */ public SequenceGroup getSelectionGroup() { @@ -649,10 +654,10 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * Set the selection group for this window. * - * @param sg - * DOCUMENT ME! + * @param sg - group holding references to sequences in this alignment view + * */ public void setSelectionGroup(SequenceGroup sg) { @@ -660,9 +665,8 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * GUI state + * @return true if conservation based shading is enabled */ public boolean getConservationSelected() { @@ -670,10 +674,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! - * + * GUI state * @param b - * DOCUMENT ME! + * enable conservation based shading */ public void setConservationSelected(boolean b) { @@ -681,9 +684,8 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * GUI state + * @return true if percent identity threshold is applied to shading */ public boolean getAbovePIDThreshold() { @@ -691,10 +693,10 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * - * @param b - * DOCUMENT ME! + * + * @param b indicate if percent identity threshold is applied to shading */ public void setAbovePIDThreshold(boolean b) { @@ -939,13 +941,13 @@ public class AlignViewport implements SelectionSource { if (alignment != null && alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager() + StructureSelectionManager.getStructureSelectionManager(Desktop.instance) .removeMappings(alignment.getCodonFrames()); } this.alignment = align; if (alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager().addMappings( + StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings( alignment.getCodonFrames()); } } @@ -1562,90 +1564,7 @@ public class AlignViewport implements SelectionSource public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth() - 1; - } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for (i = 0; i < iSize; i++) - { - selseqs[i] = new SeqCigar(seqs[i], start, end); - } - selection = new CigarArray(selseqs); - // now construct the CigarArray operations - if (hasHiddenColumns) - { - Vector regions = colSel.getHiddenColumns(); - int[] region; - int hideStart, hideEnd; - int last = start; - for (int j = 0; last < end & j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - // edit hidden regions to selection range - if (hideStart < last) - { - if (hideEnd > last) - { - hideStart = last; - } - else - { - continue; - } - } - - if (hideStart > end) - { - break; - } - - if (hideEnd > end) - { - hideEnd = end; - } - - if (hideStart > hideEnd) - { - break; - } - /** - * form operations... - */ - if (last < hideStart) - { - selection.addOperation(CigarArray.M, hideStart - last); - } - selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); - last = hideEnd + 1; - } - // Final match if necessary. - if (last < end) - { - selection.addOperation(CigarArray.M, end - last + 1); - } - } - else - { - selection.addOperation(CigarArray.M, end - start + 1); - } - return selection; + return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null)); } /** @@ -1656,21 +1575,24 @@ public class AlignViewport implements SelectionSource * boolean true to just return the selected view * @return AlignmentView */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) { - // JBPNote: - // this is here because the AlignmentView constructor modifies the - // CigarArray - // object. Refactoring of Cigar and alignment view representation should - // be done to remove redundancy. - CigarArray aligview = getViewAsCigars(selectedOnly); - if (aligview != null) - { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? selectionGroup - .getStartRes() : 0); - } - return null; + return getAlignmentView(selectedOnly, false); + } + + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @param markGroups + * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) + * @return AlignmentView + */ + public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups) + { + return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups); } /** @@ -1852,8 +1774,8 @@ public class AlignViewport implements SelectionSource { Alignment al = (Alignment) alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, al - .getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); c.verdict(false, ConsPercGaps); @@ -1867,8 +1789,8 @@ public class AlignViewport implements SelectionSource SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme) sg.cs).resetClustalX(sg - .getSequences(hiddenRepSequences), sg.getWidth()); + ((ClustalxColourScheme) sg.cs).resetClustalX( + sg.getSequences(hiddenRepSequences), sg.getWidth()); } sg.recalcConservation(); } @@ -2093,32 +2015,34 @@ public class AlignViewport implements SelectionSource /** * checks current SelectionGroup against record of last hash value, and * updates record. + * @param b update the record of last hash value * - * @return true if SelectionGroup changed since last call + * @return true if SelectionGroup changed since last call (when b is true) */ - boolean isSelectionGroupChanged() + boolean isSelectionGroupChanged(boolean b) { - int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); - if (hc != sgrouphash) + int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode(); + if (hc!=-1 && hc != sgrouphash) { - sgrouphash = hc; + if (b) {sgrouphash = hc;} return true; } return false; } /** - * checks current colsel against record of last hash value, and updates + * checks current colsel against record of last hash value, and optionally updates * record. - * - * @return true if colsel changed since last call + + * @param b update the record of last hash value + * @return true if colsel changed since last call (when b is true) */ - boolean isColSelChanged() + boolean isColSelChanged(boolean b) { - int hc = (colSel == null) ? -1 : colSel.hashCode(); - if (hc != colselhash) + int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode(); + if (hc!=-1 && hc != colselhash) { - colselhash = hc; + if (b) {colselhash = hc;} return true; } return false; @@ -2127,7 +2051,7 @@ public class AlignViewport implements SelectionSource public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sendSelection( + .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); } @@ -2319,4 +2243,43 @@ public class AlignViewport implements SelectionSource } } } + + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(Desktop.instance); + } + + /** + * + * @param pdbEntries + * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + { + ArrayList seqvectors = new ArrayList(); + for (PDBEntry pdb: pdbEntries) { + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) + { + Vector pdbs = alignment.getSequenceAt(i) + .getDatasetSequence().getPDBId(); + if (pdbs == null) + continue; + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) + { + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq=alignment.getSequenceAt(i))) + seqs.add(sq); + + continue; + } + } + } + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + } }