X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5ac946ad23d4dcbb69c2c01bc4e42542095a57e8;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=f386bf323d75a45aef6eb924dc0d6ca7e7a58895;hpb=c16d6b192b294503d2bd16294454cfe136426e7d;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index f386bf3..5ac946a --- 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, J Engelhardt, LM Lui, 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; @@ -131,24 +132,32 @@ public class AlignViewport implements SelectionSource boolean cursorMode = false; /** - * Keys are the feature types which are - * currently visible. Note: Values are not used! + * Keys are the feature types which are currently visible. Note: Values are + * not used! */ Hashtable featuresDisplayed = null; /** DOCUMENT ME!! */ public Hashtable[] hconsensus; + public Hashtable[] hStrucConsensus; + AlignmentAnnotation consensus; + AlignmentAnnotation strucConsensus; + AlignmentAnnotation conservation; AlignmentAnnotation quality; + AlignmentAnnotation[] groupConsensus; + AlignmentAnnotation[] groupConservation; - + boolean autoCalculateConsensus = true; + boolean autoCalculateStrucConsensus = true; + /** DOCUMENT ME!! */ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! @@ -193,29 +202,41 @@ 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(); } @@ -224,9 +245,9 @@ 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) { @@ -234,47 +255,69 @@ public class AlignViewport implements SelectionSource if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null && hiddenColumns.getHiddenColumns().size()>0) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; - } else { + } + 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 && hiddenColumns.getHiddenColumns().size()>0) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; - } else { + } + else + { hasHiddenColumns = false; } } @@ -298,9 +341,9 @@ 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"); @@ -351,25 +394,44 @@ public class AlignViewport implements SelectionSource alignment.addAnnotation(quality); } - showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false); - + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + { - + } } - showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true); + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_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 + // 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; consensus.autoCalculated = true; + if (alignment.isNucleotide() && alignment.hasRNAStructure()) + { + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + } + if (Cache.getDefault("SHOW_IDENTITY", true)) { alignment.addAnnotation(consensus); + // TODO: Make own if for structure + if (alignment.isNucleotide() && alignment.hasRNAStructure()) + { + alignment.addAnnotation(strucConsensus); + } } + } if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -391,15 +453,18 @@ 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) { @@ -415,14 +480,20 @@ public class AlignViewport implements SelectionSource ConsensusThread consensusThread; + StrucConsensusThread strucConsensusThread; + boolean consUpdateNeeded = false; static boolean UPDATING_CONSENSUS = false; + static boolean UPDATING_STRUC_CONSENSUS = false; + static boolean UPDATING_CONSERVATION = false; boolean updatingConsensus = false; + boolean updatingStrucConsensus = false; + boolean updatingConservation = false; /** @@ -436,17 +507,13 @@ public class AlignViewport implements SelectionSource private boolean shownpfeats; /** - * consensus annotation includes all percentage for all symbols in column - */ - private boolean includeAllConsensusSymbols=true; - - /** * trigger update of conservation annotation */ 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; } @@ -501,12 +568,14 @@ 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; } @@ -515,9 +584,8 @@ public class AlignViewport implements SelectionSource hconsensus = new Hashtable[aWidth]; AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus, includeAllConsensusSymbols); - AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols); - + .getWidth(), hconsensus, true); + updateAnnotation(true); if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -539,8 +607,155 @@ 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); + } + } + } + + // --------START Structure Conservation + public void updateStrucConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (strucConsensus == null || !autoCalculateStrucConsensus) + { + return; + } + strucConsensusThread = new StrucConsensusThread(ap); + strucConsensusThread.start(); + } + + class StrucConsensusThread extends Thread + { + AlignmentPanel ap; + + public StrucConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingStrucConsensus = true; + while (UPDATING_STRUC_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_STRUC_CONSENSUS = true; + + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) + { + updatingStrucConsensus = false; + UPDATING_STRUC_CONSENSUS = false; + return; + } + + strucConsensus.annotations = null; + strucConsensus.annotations = new Annotation[aWidth]; + + hStrucConsensus = new Hashtable[aWidth]; + + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation rnaStruc = null; + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + rnaStruc = aa[i]; + break; + } + } + + AlignmentAnnotation rna = ap.av.getAlignment() + .getAlignmentAnnotation()[0]; + StructureFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hStrucConsensus, true, rnaStruc); + // TODO AlignmentAnnotation rnaStruc!!! + updateAnnotation(true); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hStrucConsensus); + } + + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(strucConsensus); + + strucConsensus = null; + hStrucConsensus = null; + new OOMWarning("calculating structure consensus", error); + } + UPDATING_STRUC_CONSENSUS = false; + updatingStrucConsensus = false; + + if (ap != null) + { + 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 + || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null)) + { + StructureFrequency.completeConsensus(strucConsensus, + hStrucConsensus, 0, hStrucConsensus.length, false, + showSequenceLogo); + } + } } + // --------END Structure Conservation + /** * get the consensus sequence as displayed under the PID consensus annotation * row. @@ -580,9 +795,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return null or the currently selected sequence region */ public SequenceGroup getSelectionGroup() { @@ -590,20 +805,21 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * Set the selection group for this window. * * @param sg - * DOCUMENT ME! + * - group holding references to sequences in this alignment view + * */ public void setSelectionGroup(SequenceGroup sg) { - selectionGroup = sg; + selectionGroup = sg; } /** - * DOCUMENT ME! + * GUI state * - * @return DOCUMENT ME! + * @return true if conservation based shading is enabled */ public boolean getConservationSelected() { @@ -611,10 +827,10 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * * @param b - * DOCUMENT ME! + * enable conservation based shading */ public void setConservationSelected(boolean b) { @@ -622,9 +838,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * - * @return DOCUMENT ME! + * @return true if percent identity threshold is applied to shading */ public boolean getAbovePIDThreshold() { @@ -632,10 +848,11 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state + * * * @param b - * DOCUMENT ME! + * indicate if percent identity threshold is applied to shading */ public void setAbovePIDThreshold(boolean b) { @@ -676,7 +893,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGlobalColourScheme(ColourSchemeI cs) { @@ -697,7 +914,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartRes(int res) { @@ -708,7 +925,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartSeq(int seq) { @@ -719,7 +936,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndRes(int res) { @@ -742,7 +959,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -773,7 +990,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param f - * DOCUMENT ME! + * DOCUMENT ME! */ public void setFont(Font f) { @@ -801,7 +1018,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -822,7 +1039,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param h - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -843,7 +1060,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -874,20 +1091,20 @@ 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() - .removeMappings(alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); } this.alignment = align; if (alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager().addMappings( - alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); } } @@ -895,7 +1112,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -906,7 +1123,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -917,7 +1134,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -938,7 +1155,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -949,7 +1166,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -1000,7 +1217,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param gap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1014,7 +1231,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param thresh - * DOCUMENT ME! + * DOCUMENT ME! */ public void setThreshold(int thresh) { @@ -1035,7 +1252,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param inc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setIncrement(int inc) { @@ -1066,7 +1283,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1087,7 +1304,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourAppliesToAllGroups(boolean b) { @@ -1118,7 +1335,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1139,7 +1356,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1180,7 +1397,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1191,7 +1408,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1202,7 +1419,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { @@ -1213,7 +1430,7 @@ 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) @@ -1225,7 +1442,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1237,11 +1454,11 @@ 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) @@ -1459,9 +1676,9 @@ 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 @@ -1480,8 +1697,8 @@ public class AlignViewport implements SelectionSource */ public SequenceI[] getSequenceSelection() { - SequenceI[] sequences=null; - if (selectionGroup!=null) + SequenceI[] sequences = null; + if (selectionGroup != null) { sequences = selectionGroup.getSequencesInOrder(alignment); } @@ -1503,90 +1720,23 @@ 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; - } + return new jalview.datamodel.CigarArray(alignment, + (hasHiddenColumns ? colSel : null), + (selectedRegionOnly ? selectionGroup : null)); + } - 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 a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @return AlignmentView + */ + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly) + { + return getAlignmentView(selectedOnly, false); } /** @@ -1594,24 +1744,18 @@ 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 + * @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 */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly, boolean markGroups) { - // 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 new AlignmentView(alignment, colSel, selectionGroup, + hasHiddenColumns, selectedOnly, markGroups); } /** @@ -1721,22 +1865,22 @@ 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) @@ -1751,6 +1895,10 @@ public class AlignViewport implements SelectionSource { updateConsensus(ap); } + if (autoCalculateStrucConsensus) + { + updateStrucConsensus(ap); + } // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); @@ -1848,8 +1996,8 @@ 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) @@ -1888,7 +2036,7 @@ 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 */ @@ -1946,11 +2094,12 @@ 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; } /** @@ -1970,14 +2119,18 @@ 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 @@ -1986,6 +2139,7 @@ public class AlignViewport implements SelectionSource { return hasHiddenRows; } + /** * * @return true if view has hidden columns @@ -1994,85 +2148,128 @@ 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)) + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) { - if (!wholewidth && alignment.getWidth()==(1+sge-sgs)) + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) { - // do nothing + // do nothing return; } - if (colSel==null) + if (colSel == null) { colSel = new ColumnSelection(); } - for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) { + 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()][]); + } + + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; } }