X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=e9d418e84f03d697b9b7c1cc726d5eddab8beb22;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=9d19cf3015a97a5c80aadd7e580feccb03452666;hpb=9b7ee35c6b9909b030b5b04e33266acf8d5ad637;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 9d19cf3..e9d418e 100644 --- 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. * @@ -282,16 +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 @@ -301,10 +303,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme } if (av.applet.debug) { // DEBUG - System.out.println("DEBUG: scroll: 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]; @@ -322,45 +325,75 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme } public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview) { - int start=-1; - if (av.hasHiddenColumns) + 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) { - if (!scrollToNearest && !av.colSel.isVisible(ostart)) + if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart)) { // 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 { @@ -423,7 +456,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme apvscroll.addNotify(); hscroll.addNotify(); validate(); - repaint(); + paintAlignment(true); } /** * calculate the annotation dimensions and refresh slider values accordingly. @@ -463,6 +496,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); annotationPanelHolder.setSize(new Dimension(d.width, height)); seqPanelHolder.setSize(d.width,seqandannot-height); + seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); int s=apvscroll.getValue(); if (s>mheight-height) { @@ -555,16 +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; @@ -581,6 +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; } @@ -596,18 +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); @@ -731,9 +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; } @@ -881,10 +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()); + ; // 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) { @@ -893,18 +931,16 @@ 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; } } } - SequenceGroup sg; - if (gr != null) + if (av.getAlignment().getGroups()!= null) { - for (int g = 0; g < gr.size(); g++) + for (SequenceGroup sg:av.getAlignment().getGroups()) { updateCalcs = false; - sg = (SequenceGroup) gr.elementAt(g); if (applyGlobalSettings || !oldrfs.containsKey(sg)) { // set defaults for this group's conservation/consensus @@ -914,12 +950,12 @@ 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) @@ -935,12 +971,19 @@ 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(); + } }