X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=eedc8637a906cbebedf5954e85bad31a334e463f;hb=b76d0ffcb6effa94954f75e030d1d67c890134eb;hp=70ca6f29c734fb45faa97dcea94beb8330f4146a;hpb=eeaf210a324ea2677c8267531ffb78e1c19fada1;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 70ca6f2..eedc863 100755 --- 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 2.5) + * Copyright (C) 2010 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 @@ -130,8 +129,10 @@ 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!! */ @@ -142,9 +143,11 @@ public class AlignViewport implements SelectionSource AlignmentAnnotation conservation; AlignmentAnnotation quality; + AlignmentAnnotation[] groupConsensus; + AlignmentAnnotation[] groupConservation; - + boolean autoCalculateConsensus = true; /** DOCUMENT ME!! */ @@ -191,29 +194,41 @@ 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(); } @@ -222,9 +237,9 @@ 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) { @@ -232,45 +247,71 @@ 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(); } @@ -292,9 +333,9 @@ 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"); @@ -345,8 +386,20 @@ 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; @@ -377,15 +430,18 @@ 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) { @@ -427,7 +483,8 @@ 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; } @@ -483,9 +540,9 @@ public class AlignViewport implements SelectionSource try { int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null - // pointer - // possibility - // here. + // pointer + // possibility + // here. if (aWidth < 0) { return; @@ -496,9 +553,9 @@ public class AlignViewport implements SelectionSource hconsensus = new Hashtable[aWidth]; AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation); - + .getWidth(), hconsensus, true); + updateAnnotation(true); + if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -520,6 +577,27 @@ 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); + } + } } /** @@ -574,11 +652,11 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param sg - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSelectionGroup(SequenceGroup sg) { - selectionGroup = sg; + selectionGroup = sg; } /** @@ -595,7 +673,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setConservationSelected(boolean b) { @@ -616,7 +694,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAbovePIDThreshold(boolean b) { @@ -657,7 +735,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGlobalColourScheme(ColourSchemeI cs) { @@ -678,7 +756,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartRes(int res) { @@ -689,7 +767,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartSeq(int seq) { @@ -700,7 +778,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndRes(int res) { @@ -723,7 +801,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -754,7 +832,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param f - * DOCUMENT ME! + * DOCUMENT ME! */ public void setFont(Font f) { @@ -782,7 +860,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -803,7 +881,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param h - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -824,7 +902,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -855,7 +933,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param align - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { @@ -876,7 +954,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -887,7 +965,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -898,7 +976,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -919,7 +997,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -930,7 +1008,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -981,7 +1059,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param gap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -995,7 +1073,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param thresh - * DOCUMENT ME! + * DOCUMENT ME! */ public void setThreshold(int thresh) { @@ -1016,7 +1094,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param inc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setIncrement(int inc) { @@ -1047,7 +1125,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1068,7 +1146,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourAppliesToAllGroups(boolean b) { @@ -1099,7 +1177,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1120,7 +1198,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1161,7 +1239,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1172,7 +1250,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1183,7 +1261,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { @@ -1194,7 +1272,7 @@ 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) @@ -1206,7 +1284,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1218,11 +1296,11 @@ 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) @@ -1440,9 +1518,9 @@ 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 @@ -1461,8 +1539,8 @@ public class AlignViewport implements SelectionSource */ public SequenceI[] getSequenceSelection() { - SequenceI[] sequences=null; - if (selectionGroup!=null) + SequenceI[] sequences = null; + if (selectionGroup != null) { sequences = selectionGroup.getSequencesInOrder(alignment); } @@ -1494,7 +1572,7 @@ public class AlignViewport implements SelectionSource seqs = selectionGroup.getSequencesInOrder(alignment); start = selectionGroup.getStartRes(); end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor + // SeqCigar constructor } else { @@ -1575,7 +1653,7 @@ 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) @@ -1702,22 +1780,22 @@ 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) @@ -1829,8 +1907,8 @@ 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) @@ -1869,7 +1947,7 @@ 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 */ @@ -1927,11 +2005,12 @@ 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; } /** @@ -1951,14 +2030,18 @@ 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 @@ -1967,6 +2050,7 @@ public class AlignViewport implements SelectionSource { return hasHiddenRows; } + /** * * @return true if view has hidden columns @@ -1975,85 +2059,115 @@ 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. + * checks current SelectionGroup against record of last hash value, and + * updates record. + * * @return true if SelectionGroup changed since last call */ - boolean isSelectionGroupChanged() { - int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode(); - if (hc!=sgrouphash) + boolean isSelectionGroupChanged() + { + int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); + if (hc != sgrouphash) { sgrouphash = hc; return true; } return false; } + /** - * checks current colsel against record of last hash value, and updates record. + * checks current colsel against record of last hash value, and updates + * record. + * * @return true if colsel changed since last call */ - boolean isColSelChanged() { - int hc=(colSel==null) ? -1 : colSel.hashCode(); - if (hc!=colselhash) + boolean isColSelChanged() + { + int hc = (colSel == null) ? -1 : colSel.hashCode(); + if (hc != colselhash) { 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().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); + } + } + } }