X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=13f66d973ffeaf84e2085f32bd7e07f85db678c4;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=8c23e4d0121f620ad5e2dd6d62f52827c1f34668;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 8c23e4d..13f66d9 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, 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 program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ /* * Jalview - A Sequence Alignment Editor and Viewer @@ -41,6 +40,7 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.StructureSelectionManagerProvider; import jalview.bin.*; @@ -49,14 +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; @@ -130,8 +131,10 @@ public class AlignViewport implements SelectionSource boolean cursorMode = false; - // The following vector holds the features which are - // currently visible, in the correct order or rendering + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ Hashtable featuresDisplayed = null; /** DOCUMENT ME!! */ @@ -143,6 +146,10 @@ public class AlignViewport implements SelectionSource AlignmentAnnotation quality; + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + boolean autoCalculateConsensus = true; /** DOCUMENT ME!! */ @@ -189,29 +196,41 @@ public class AlignViewport implements SelectionSource /** * Creates a new AlignViewport object. * - * @param al alignment to view + * @param al + * alignment to view */ public AlignViewport(AlignmentI al) { setAlignment(al); init(); } + /** * Create a new AlignViewport object with a specific sequence set ID + * * @param al - * @param seqsetid (may be null - but potential for ambiguous constructor exception) + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) */ public AlignViewport(AlignmentI al, String seqsetid) { - this(al,seqsetid,null); + this(al, seqsetid, null); } + public AlignViewport(AlignmentI al, String seqsetid, String viewid) { sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished - if (Cache.log!=null && Cache.log.isDebugEnabled() && seqsetid!=null) { Cache.log.debug("Setting viewport's sequence set id : "+sequenceSetID); } - if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); } + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } setAlignment(al); init(); } @@ -220,9 +239,9 @@ public class AlignViewport implements SelectionSource * Create a new AlignViewport with hidden regions * * @param al - * AlignmentI + * AlignmentI * @param hiddenColumns - * ColumnSelection + * ColumnSelection */ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { @@ -230,45 +249,71 @@ public class AlignViewport implements SelectionSource if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; } + else + { + hasHiddenColumns = false; + } } init(); } + /** * New viewport with hidden columns and an existing sequence set id + * * @param al * @param hiddenColumns - * @param seqsetid (may be null) + * @param seqsetid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid) + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) { - this(al,hiddenColumns,seqsetid,null); + this(al, hiddenColumns, seqsetid, null); } + /** * New viewport with hidden columns and an existing sequence set id and viewid + * * @param al * @param hiddenColumns - * @param seqsetid (may be null) - * @param viewid (may be null) + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid) + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) { sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished - if (Cache.log!=null && Cache.log.isDebugEnabled() && seqsetid!=null) { Cache.log.debug("Setting viewport's sequence set id : "+sequenceSetID); } - if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); } + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } setAlignment(al); if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; } + else + { + hasHiddenColumns = false; + } } init(); } @@ -290,9 +335,9 @@ public class AlignViewport implements SelectionSource autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); padGaps = Cache.getDefault("PAD_GAPS", true); - shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP",true); - showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP",true); - + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); String fontSize = Cache.getDefault("FONT_SIZE", "10"); @@ -343,8 +388,20 @@ public class AlignViewport implements SelectionSource alignment.addAnnotation(quality); } + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + + { + + } } - // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + // TODO: add menu option action that nulls or creates consensus object + // depending on if the user wants to see the annotation or not in a + // specific alignment consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; @@ -375,15 +432,18 @@ public class AlignViewport implements SelectionSource } wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); - showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", false); + showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", + false); sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); } /** * set the flag * * @param b - * features are displayed if true + * features are displayed if true */ public void setShowSequenceFeatures(boolean b) { @@ -395,146 +455,6 @@ public class AlignViewport implements SelectionSource return showSequenceFeatures; } - class ConservationThread extends Thread - { - AlignmentPanel ap; - - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - return; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, alignment - .getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and - // Quality - - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; - - char c; - - conservation.annotations = new Annotation[alWidth]; - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ((Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String - .valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - } - } - } catch (OutOfMemoryError error) - { - new OOMWarning("calculating conservation", error); - - conservation = null; - quality = null; - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - - } - } - ConservationThread conservationThread; ConsensusThread consensusThread; @@ -565,12 +485,13 @@ public class AlignViewport implements SelectionSource public void updateConservation(final AlignmentPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus) + if (alignment.isNucleotide() || conservation == null + || !autoCalculateConsensus) { return; } - conservationThread = new ConservationThread(ap); + conservationThread = new ConservationThread(this, ap); conservationThread.start(); } @@ -620,12 +541,14 @@ public class AlignViewport implements SelectionSource try { - int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null - // pointer - // possibility - // here. - if (aWidth < 0) + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) { + updatingConsensus = false; + UPDATING_CONSENSUS = false; return; } @@ -633,38 +556,9 @@ public class AlignViewport implements SelectionSource consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } + AAFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hconsensus, true); + updateAnnotation(true); if (globalColourScheme != null) { @@ -687,6 +581,28 @@ public class AlignViewport implements SelectionSource ap.paintAlignment(true); } } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + 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. + if (immediate + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } } /** @@ -728,9 +644,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return null or the currently selected sequence region */ public SequenceGroup getSelectionGroup() { @@ -738,20 +654,19 @@ 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) { - selectionGroup = sg; + selectionGroup = sg; } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * GUI state + * @return true if conservation based shading is enabled */ public boolean getConservationSelected() { @@ -759,10 +674,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! - * + * GUI state * @param b - * DOCUMENT ME! + * enable conservation based shading */ public void setConservationSelected(boolean b) { @@ -770,9 +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() { @@ -780,10 +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) { @@ -824,7 +737,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGlobalColourScheme(ColourSchemeI cs) { @@ -845,7 +758,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartRes(int res) { @@ -856,7 +769,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartSeq(int seq) { @@ -867,7 +780,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndRes(int res) { @@ -890,7 +803,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -921,7 +834,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param f - * DOCUMENT ME! + * DOCUMENT ME! */ public void setFont(Font f) { @@ -949,7 +862,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -970,7 +883,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param h - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -991,7 +904,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -1022,19 +935,19 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param align - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { 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()); } } @@ -1043,7 +956,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -1054,7 +967,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -1065,7 +978,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -1086,7 +999,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -1097,7 +1010,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -1148,7 +1061,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param gap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1162,7 +1075,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param thresh - * DOCUMENT ME! + * DOCUMENT ME! */ public void setThreshold(int thresh) { @@ -1183,7 +1096,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param inc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setIncrement(int inc) { @@ -1214,7 +1127,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1235,7 +1148,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourAppliesToAllGroups(boolean b) { @@ -1266,7 +1179,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1287,7 +1200,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1328,7 +1241,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1339,7 +1252,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1350,7 +1263,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { @@ -1361,7 +1274,7 @@ public class AlignViewport implements SelectionSource * Property change listener for changes in alignment * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void addPropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1373,7 +1286,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1385,11 +1298,11 @@ public class AlignViewport implements SelectionSource * Property change listener for changes in alignment * * @param prop - * DOCUMENT ME! + * DOCUMENT ME! * @param oldvalue - * DOCUMENT ME! + * DOCUMENT ME! * @param newvalue - * DOCUMENT ME! + * DOCUMENT ME! */ public void firePropertyChange(String prop, Object oldvalue, Object newvalue) @@ -1607,9 +1520,9 @@ public class AlignViewport implements SelectionSource for (int i = 0; i < sequences.length; i++) { sequences[i] = new Sequence(sequences[i], annots); // construct new - // sequence with - // subset of visible - // annotation + // sequence with + // subset of visible + // annotation } } else @@ -1628,8 +1541,8 @@ public class AlignViewport implements SelectionSource */ public SequenceI[] getSequenceSelection() { - SequenceI[] sequences=null; - if (selectionGroup!=null) + SequenceI[] sequences = null; + if (selectionGroup != null) { sequences = selectionGroup.getSequencesInOrder(alignment); } @@ -1651,90 +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)); } /** @@ -1742,24 +1572,27 @@ public class AlignViewport implements SelectionSource * to an analysis function * * @param selectedOnly - * boolean true to just return the selected view + * 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); } /** @@ -1869,22 +1702,22 @@ public class AlignViewport implements SelectionSource return sequenceSetID; } + /** - * unique viewId for synchronizing state with stored Jalview Project + * unique viewId for synchronizing state with stored Jalview Project * */ - private String viewId=null; + private String viewId = null; - public String getViewId() { - if (viewId==null) + if (viewId == null) { - viewId = this.getSequenceSetId()+"."+this.hashCode()+""; + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; } return viewId; } - + public void alignmentChanged(AlignmentPanel ap) { if (padGaps) @@ -1941,8 +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); @@ -1956,8 +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(); } @@ -1996,8 +1829,8 @@ public class AlignViewport implements SelectionSource * returns the visible column regions of the alignment * * @param selectedRegionOnly - * true to just return the contigs intersecting with the - * selected area + * true to just return the contigs intersecting with the selected + * area * @return */ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) @@ -2036,7 +1869,7 @@ public class AlignViewport implements SelectionSource * the undo and redo list. * * @param undoredo - * the stored set of hashcodes as returned by getUndoRedoHash + * the stored set of hashcodes as returned by getUndoRedoHash * @return true if the hashcodes differ (ie the alignment has been edited) or * the stored hashcode array differs in size */ @@ -2094,11 +1927,12 @@ public class AlignViewport implements SelectionSource } /** - * enable or disable the display of Database Cross References in the sequence ID tooltip - */ + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ public void setShowDbRefs(boolean show) { - showdbrefs=show; + showdbrefs = show; } /** @@ -2118,14 +1952,18 @@ public class AlignViewport implements SelectionSource { return shownpfeats; } + /** - * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip - * @param show + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show */ public void setShowNpFeats(boolean show) { - shownpfeats=show; + shownpfeats = show; } + /** * * @return true if view has hidden rows @@ -2134,6 +1972,7 @@ public class AlignViewport implements SelectionSource { return hasHiddenRows; } + /** * * @return true if view has hidden columns @@ -2142,85 +1981,117 @@ public class AlignViewport implements SelectionSource { return hasHiddenColumns; } + /** * when set, view will scroll to show the highlighted position */ - public boolean followHighlight=true; + public boolean followHighlight = true; + /** - * @return true if view should scroll to show the highlighted region of a sequence + * @return true if view should scroll to show the highlighted region of a + * sequence * @return */ - public boolean getFollowHighlight() { + public boolean getFollowHighlight() + { return followHighlight; } - public boolean followSelection=true; + + public boolean followSelection = true; + /** - * @return true if view selection should always follow the selections broadcast by other selection sources + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public boolean getFollowSelection() { + public boolean getFollowSelection() + { return followSelection; } - private long sgrouphash=-1,colselhash=-1; + + private long sgrouphash = -1, colselhash = -1; boolean showSeqFeaturesHeight; + /** - * checks current SelectionGroup against record of last hash value, and updates record. - * @return true if SelectionGroup changed since last call + * 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 (when b is true) */ - boolean isSelectionGroupChanged() { - int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode(); - if (hc!=sgrouphash) + boolean isSelectionGroupChanged(boolean b) + { + 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 record. - * @return true if colsel changed since last call + * checks current colsel against record of last hash value, and optionally updates + * record. + + * @param b update the record of last hash value + * @return true if colsel changed since last call (when b is true) */ - boolean isColSelChanged() { - int hc=(colSel==null) ? -1 : colSel.hashCode(); - if (hc!=colselhash) + boolean isColSelChanged(boolean b) + { + 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; } + public void sendSelection() { - jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); } + public void setShowSequenceFeaturesHeight(boolean selected) { - showSeqFeaturesHeight = selected; + showSeqFeaturesHeight = selected; } + public boolean getShowSequenceFeaturesHeight() { - return showSeqFeaturesHeight; + return showSeqFeaturesHeight; } - boolean showUnconserved=false; + + boolean showUnconserved = false; + public boolean getShowUnconserved() { return showUnconserved; } + public void setShowUnconserved(boolean showunconserved) { - showUnconserved=showunconserved; + showUnconserved = showunconserved; } + /** * return the alignPanel containing the given viewport. Use this to get the * components currently handling the given viewport. + * * @param av - * @return null or an alignPanel guaranteed to have non-null alignFrame reference + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference */ public AlignmentPanel getAlignPanel() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this.getSequenceSetId()); - AlignmentPanel ap=null; - for (int p=0;aps!=null && p= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } + + 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()][]); + } }