X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=99c7c72e5f01bda5e660bbb0caf666a19151b19d;hb=acfc0d246c770a0a1e9cea7cb7fc40cf11f03ca7;hp=bbd9f72b8550e3a3855d46136ff8ea18f14b1aba;hpb=106634777c0910504d9c1617d6307b70581fd3c8;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index bbd9f72..99c7c72 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -20,12 +20,15 @@ package jalview.gui; import java.beans.*; import java.io.*; +import java.util.Hashtable; +import java.util.Vector; import java.awt.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; +import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; @@ -70,9 +73,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! + * DOCUMENT ME! * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -224,75 +227,99 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param results - * DOCUMENT ME! + * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { scrollToPosition(results); seqPanel.seqCanvas.highlightSearchResults(results); } + /** - * scroll the view to show the position of the highlighted - * region in results (if any) and redraw the overview + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * * @param results */ - public boolean scrollToPosition(SearchResults results) { + public boolean scrollToPosition(SearchResults results) + { return scrollToPosition(results, true); } + /** - * scroll the view to show the position of the highlighted - * region in results (if any) + * scroll the view to show the position of the highlighted region in results + * (if any) + * * @param results - * @param redrawOverview - when set, the overview will be recalculated (takes longer) + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { - // TODO: properly locate search results in view when large numbers of hidden columns exist before highlighted region + public boolean scrollToPosition(SearchResults results, + boolean redrawOverview) + { + int startv, endv, starts, ends, width; + // TODO: properly locate search results in view when large numbers of hidden + // columns exist before highlighted region // do we need to scroll the panel? - if (results != null && results.getSize()>0) + // TODO: tons of nullpointereexceptions raised here. + if (results != null && results.getSize() > 0 && av != null + && av.alignment != null) { int seqIndex = av.alignment.findIndex(results); - if (seqIndex==-1) + if (seqIndex == -1) { return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); - - int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); - if (r==null) + + int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq, + // seq.getStart(), + // seq.getEnd()); + // TODO: VAMSAS: fix hidden column issue where scroll to left from C + // terminus is not visible + if (r == null) { return false; } int start = r[0]; int end = r[1]; - if (start<0) + if (start < 0) { return false; } - if (end==seq.getEnd()) + if (end == seq.getEnd()) { return false; } if (!av.wrapAlignment) { - if ((av.getStartRes() >= start) - || (av.getEndRes() <= end)) + if ((startv = av.getStartRes()) >= start) + { + setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) { - setScrollValues(start-1, seqIndex); - } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)) + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), seqIndex); } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } } else { scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel!=null) + if (!redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); - } + } paintAlignment(!redrawOverview); return true; } @@ -301,7 +328,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int cwidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth)) + if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; @@ -323,7 +350,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param op - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -334,7 +361,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAnnotationVisible(boolean b) { @@ -374,6 +401,7 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); + addNotify(); repaint(); } @@ -381,7 +409,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param wrap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { @@ -439,7 +467,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param right - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -475,13 +503,14 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param x - * DOCUMENT ME! + * DOCUMENT ME! * @param y - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScrollValues(int x, int y) { - if (av==null || av.alignment==null) + // System.err.println("Scroll to "+x+","+y); + if (av == null || av.alignment == null) { return; } @@ -536,7 +565,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -647,7 +676,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -690,16 +719,16 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pf - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -723,18 +752,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -870,18 +899,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -1260,4 +1289,96 @@ public class AlignmentPanel extends GAlignmentPanel implements return height; } + + /** + * close the panel - deregisters all listeners and nulls any references to + * alignment data. + */ + public void closePanel() + { + jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager + .getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); + PaintRefresher.RemoveComponent(seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(idPanel.idCanvas); + PaintRefresher.RemoveComponent(this); + if (av != null) + { + av.alignment = null; + av = null; + } + else + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.warn("Closing alignment panel which is already closed."); + } + } + } + + /** + * hides or shows dynamic annotation rows based on groups and av state flags + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + public void updateAnnotation(boolean applyGlobalSettings) + { + boolean updateCalcs = false; + boolean conv = av.isShowGroupConservation(); + boolean cons = av.isShowGroupConsensus(); + boolean showprf = av.isShowConsensusProfile(); + boolean showConsHist = av.isShowConsensusHistogram(); + + boolean sortg = true; + + // remove old automatic annotation + // add any new annotation + + Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); + // intersect alignment annotation with alignment groups + + AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + Hashtable oldrfs = new Hashtable(); + for (int an = 0; an < aan.length; an++) + { + if (aan[an].autoCalculated && aan[an].groupRef != null) + { + oldrfs.put(aan[an].groupRef, aan[an].groupRef); + av.alignment.deleteAnnotation(aan[an]); + aan[an] = null; + } + } + SequenceGroup sg; + for (int g = 0; g < gr.size(); g++) + { + updateCalcs = false; + sg = (SequenceGroup) gr.elementAt(g); + if (applyGlobalSettings || !oldrfs.containsKey(sg)) + { + // set defaults for this group's conservation/consensus + sg.setIncludeAllConsSymbols(showprf); + sg.setShowConsensusHistogram(showConsHist); + } + if (conv) + { + updateCalcs = true; + av.alignment.addAnnotation(sg.getConservationRow(),0); + } + if (cons) + { + updateCalcs = true; + av.alignment.addAnnotation(sg.getConsensus(),0); + } + // refresh the annotation rows + if (updateCalcs) + { + sg.recalcConservation(); + } + } + oldrfs.clear(); + adjustAnnotationHeight(); + } }