X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=99084ba1c7c519c50e50b2ae231feaa4aec89174;hb=6bd9630607bd38aaf9b42738a0ae90de8fe5c6e8;hp=e4b9b595442aebd4e812b23f39a24551cafbf647;hpb=2143ce8c4c9af885bc6d455655775d1ecb62acae;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index e4b9b59..99084ba --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -24,6 +24,7 @@ import java.util.Vector; import jalview.api.AlignmentViewPanel; import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { @@ -48,7 +49,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme // this value is set false when selection area being dragged boolean fastPaint = true; - + + public void finalize() { + alignFrame=null; + av=null; + seqPanel=null; + seqPanelHolder=null; + sequenceHolderPanel=null; + scalePanel=null; + scalePanelHolder=null; + annotationPanel=null; + annotationPanelHolder=null; + annotationSpaceFillerHolder=null; + } public AlignmentPanel(AlignFrame af, final AlignViewport av) { try @@ -92,8 +105,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme public void componentResized(ComponentEvent evt) { setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height>0 && annotationPanelHolder.getSize().height>0) { + validateAnnotationDimensions(false); + } repaint(); } + }); Dimension d = calculateIdWidth(); @@ -160,6 +177,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme Dimension d = calculateIdWidth(); d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height); alabels.setSize(d.width + 4, ap); + idPanel.idCanvas.setSize(d); hscrollFillerPanel.setSize(d); @@ -264,16 +282,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { + // do we need to scroll the panel? if (results != null && results.getSize() > 0) { - int seqIndex = av.alignment.findIndex(results); + AlignmentI alignment=av.getAlignment(); + int seqIndex = alignment.findIndex(results); if (seqIndex == -1) { return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int[] r = results.getResults(seq, 0,av.alignment.getWidth()); + SequenceI seq = alignment.getSequenceAt(seqIndex); + int[] r = results.getResults(seq, 0,alignment.getWidth()); if (r == null) { if (av.applet.debug) {// DEBUG @@ -283,10 +303,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme } if (av.applet.debug) { // DEBUG - System.out.println("DEBUG: scroll didn't happen: start=" + r[0] + /*System.out.println("DEBUG: scroll: start=" + r[0] + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] + " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() + " hextent=" + hextent); + */ } int start = r[0]; int end = r[1]; @@ -298,50 +319,86 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme { return false; } - if (av.hasHiddenColumns) + return scrollTo(start, end, seqIndex, false, redrawOverview); + } + return true; + } + public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends, width; + + int start=-1; + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(ostart); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); - if (start == end) + if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart)) { - if (!av.colSel.isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } + // don't scroll - position isn't visible + return false; } } - if (!av.wrapAlignment) - { + } + else + { + start = ostart; + } + if (!av.wrapAlignment) + { + /* + int spos=av.getStartRes(),sqpos=av.getStartSeq(); + if ((startv = av.getStartRes()) >= start) + { + spos=start-1; +// seqIn +// setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { +// setScrollValues(spos=startv + 1 + end - endv, seqIndex); + spos=startv + 1 + end - endv; + } + else if ((starts = av.getStartSeq()) > seqIndex) + { + setScrollValues(av.getStartRes(), seqIndex); + } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } + + /* */ if ((av.getStartRes() > end) || (av.getEndRes() < start) || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) { - if (start > av.alignment.getWidth() - hextent) + if (start > av.getAlignment().getWidth() - hextent) { - start = av.alignment.getWidth() - hextent; + start = av.getAlignment().getWidth() - hextent; if (start < 0) { start = 0; } } - if (seqIndex > av.alignment.getHeight() - vextent) + if (seqIndex > av.getAlignment().getHeight() - vextent) { - seqIndex = av.alignment.getHeight() - vextent; + seqIndex = av.getAlignment().getHeight() - vextent; if (seqIndex < 0) { seqIndex = 0; } } + // System.out.println("trying to scroll to: "+start+" "+seqIndex); setScrollValues(start, seqIndex); - } + }/**/ } else { scrollToWrappedVisible(start); } - } if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); @@ -399,42 +456,53 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme apvscroll.addNotify(); hscroll.addNotify(); validate(); - addNotify(); - repaint(); + paintAlignment(true); } /** * calculate the annotation dimensions and refresh slider values accordingly. * need to do repaints/notifys afterwards. */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + boolean modified=false; int height = annotationPanel.calcPanelHeight(); + int minsize=0; if (hscroll.isVisible()) { - height += hscroll.getPreferredSize().height; + height += (minsize=hscroll.getPreferredSize().height); + } + if (apvscroll.isVisible()) { + minsize+=apvscroll.getPreferredSize().height; } int mheight = height; + Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize(); + int seqandannot=d.height-scalePanelHolder.getSize().height; // sets initial preferred height - if ((height+40) > getSize().height / 2) + if ((height+40) > seqandannot / 2) { - height = getSize().height / 2; + height = seqandannot / 2; } if (!adjustPanelHeight) { // maintain same window layout whilst updating sliders - height=seqPanelHolder.getSize().height; + height=annotationPanelHolder.getSize().height; + } + + if (seqandannot-height<5) + { + height = seqandannot; } - Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize(); annotationPanel.setSize(new Dimension(d.width,height)); - alabels.setSize(e.width,height); + alabels.setSize(new Dimension(e.width,height)); annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); annotationPanelHolder.setSize(new Dimension(d.width, height)); - seqPanelHolder.setSize(d.width,d.height-height); + seqPanelHolder.setSize(d.width,seqandannot-height); + seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); int s=apvscroll.getValue(); if (s>mheight-height) { s = 0; } - apvscroll.setValues(apvscroll.getValue(), height, 0, mheight); + apvscroll.setValues(s, height, 0, mheight); annotationPanel.setScrollOffset(apvscroll.getValue()); alabels.setScrollOffset(apvscroll.getValue()); } @@ -521,16 +589,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme public void setScrollValues(int x, int y) { - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { width = av.getColumnSelection().findColumnPosition(width); } - - av.setStartRes(x); - av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + if (x<0) { x = 0; }; hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; @@ -547,6 +613,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if ((hextent + x) > width) { + System.err.println("hextent was "+hextent+" and x was "+x); + x = width - hextent; } @@ -562,18 +630,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (x < 0) { + System.err.println("x was "+x); x = 0; } av.setStartSeq(y); int endSeq = y + vextent; - if (endSeq > av.alignment.getHeight()) + if (endSeq > av.getAlignment().getHeight()) { - endSeq = av.alignment.getHeight(); + endSeq = av.getAlignment().getHeight(); } av.setEndSeq(endSeq); + av.setStartRes(x); + av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + hscroll.setValues(x, hextent, 0, width); vscroll.setValues(y, vextent, 0, height); @@ -581,6 +653,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme { overviewPanel.setBoxPosition(); } + sendViewPosition(); + } @@ -658,8 +732,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme annotationPanel.fastPaint(av.getStartRes() - oldX); } } + sendViewPosition(); } + private void sendViewPosition() + { + StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq); + } public void paintAlignment(boolean updateOverview) { @@ -668,7 +747,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (updateOverview) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + .getStructureSelectionManager(av.applet).sequenceColoursChanged(this); if (overviewPanel != null) { @@ -690,9 +769,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (av.getWrapAlignment()) { - int maxwidth = av.alignment.getWidth(); + int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -840,10 +919,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme // remove old automatic annotation // add any new annotation - Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); + Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.alignment.getSequencesArray()); // intersect alignment annotation with alignment groups - AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); Hashtable oldrfs = new Hashtable(); if (aan != null) { @@ -852,7 +931,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (aan[an].autoCalculated && aan[an].groupRef != null) { oldrfs.put(aan[an].groupRef, aan[an].groupRef); - av.alignment.deleteAnnotation(aan[an]); + av.getAlignment().deleteAnnotation(aan[an]); aan[an] = null; } } @@ -873,12 +952,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (conv) { updateCalcs = true; - av.alignment.addAnnotation(sg.getConservationRow(), 0); + av.getAlignment().addAnnotation(sg.getConservationRow(), 0); } if (cons) { updateCalcs = true; - av.alignment.addAnnotation(sg.getConsensus(), 0); + av.getAlignment().addAnnotation(sg.getConsensus(), 0); } // refresh the annotation rows if (updateCalcs) @@ -894,7 +973,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme @Override public AlignmentI getAlignment() { - return av.alignment; + return av.getAlignment(); + } + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(av.applet); + } + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + // TODO: JAL-960 + System.err.println("Out of memory whilst '"+string+"'"); + error.printStackTrace(); } }