X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=e9d418e84f03d697b9b7c1cc726d5eddab8beb22;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=6d4c63b95548c3dfac2c7bb0b9d1c7e814766c85;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index 6d4c63b..e9d418e --- 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. * @@ -19,10 +19,14 @@ package jalview.appletgui; import java.awt.*; import java.awt.event.*; +import java.util.Hashtable; +import java.util.Vector; +import jalview.api.AlignmentViewPanel; import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; -public class AlignmentPanel extends Panel implements AdjustmentListener +public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { public AlignViewport av; @@ -45,7 +49,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // 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 @@ -63,8 +79,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener scalePanel = new ScalePanel(av, this); idwidthAdjuster = new IdwidthAdjuster(this); annotationPanel = new AnnotationPanel(this); + annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER); - sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH); + sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH); alabels = new AnnotationLabels(this); @@ -79,6 +96,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener fontChanged(); setScrollValues(0, 0); + apvscroll.addAdjustmentListener(this); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -87,8 +105,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void componentResized(ComponentEvent evt) { setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height>0 && annotationPanelHolder.getSize().height>0) { + validateAnnotationDimensions(false); + } repaint(); } + }); Dimension d = calculateIdWidth(); @@ -100,7 +122,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener annotationSpaceFillerHolder.setSize(d.width, annotationPanel.getSize().height); alabels.setSize(d.width, annotationPanel.getSize().height); - final AlignmentPanel ap = this; av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { @@ -152,14 +173,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener + fm.getDescent())); av.updateSequenceIdColours(); annotationPanel.image = null; - int ap = annotationPanel.adjustPanelHeight(); - annotationPanel.repaint(); + int ap = annotationPanel.adjustPanelHeight(false); 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); - + + validateAnnotationDimensions(false); + annotationPanel.repaint(); validate(); repaint(); @@ -173,6 +196,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { idPanel.idCanvas.setSize(w, h); idPanelHolder.setSize(w, idPanelHolder.getSize().height); + annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height); alabels.setSize(w, alabels.getSize().height); validate(); } @@ -224,75 +248,163 @@ public class AlignmentPanel extends Panel implements AdjustmentListener return new Dimension(idWidth, idPanel.idCanvas.getSize().height); } + /** + * Highlight the given results on the alignment. + * + */ 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 + * + * @param results + * @return false if results were not found + */ + public boolean scrollToPosition(SearchResults results) + { + return scrollToPosition(results, true); + } + + /** + * 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) + * @return false if results were not found */ - public void scrollToPosition(SearchResults results) + 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; + return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int[] r = results.getResults(seq, seq.getStart(), seq.getEnd()); + SequenceI seq = alignment.getSequenceAt(seqIndex); + int[] r = results.getResults(seq, 0,alignment.getWidth()); if (r == null) { - return; + if (av.applet.debug) {// DEBUG + System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd()); + } + return false; + } + if (av.applet.debug) { + // DEBUG + /*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]; if (start < 0) { - return; + return false; } if (end == seq.getEnd()) { - return; + return false; } - if (!av.wrapAlignment) + 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) { + if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + 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(); } - - repaint(); + paintAlignment(redrawOverview); + return true; } void scrollToWrappedVisible(int res) @@ -321,12 +433,80 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationPanel.setVisible(b); + annotationPanelHolder.setVisible(b); } validate(); repaint(); } - + + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ + public void adjustAnnotationHeight() + { + // TODO: display vertical annotation scrollbar if necessary + // this is called after loading new annotation onto alignment + if (alignFrame.getSize().height == 0) + { + System.out.println("NEEDS FIXING"); + } + fontChanged(); + validateAnnotationDimensions(true); + apvscroll.addNotify(); + hscroll.addNotify(); + validate(); + 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 += (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) > seqandannot / 2) + { + height = seqandannot / 2; + } + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height=annotationPanelHolder.getSize().height; + } + + if (seqandannot-height<5) + { + height = seqandannot; + } + annotationPanel.setSize(new Dimension(d.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,seqandannot-height); + seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); + int s=apvscroll.getValue(); + if (s>mheight-height) + { + s = 0; + } + apvscroll.setValues(s, height, 0, mheight); + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + } + public void setWrapAlignment(boolean wrap) { av.startSeq = 0; @@ -338,12 +518,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (wrap) { - annotationPanel.setVisible(false); + annotationPanelHolder.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { - annotationPanel.setVisible(true); + annotationPanelHolder.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } @@ -409,20 +589,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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; - + if (hextent > width) { hextent = width; @@ -435,6 +613,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if ((hextent + x) > width) { + System.err.println("hextent was "+hextent+" and x was "+x); + x = width - hextent; } @@ -450,18 +630,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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); @@ -469,6 +653,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { overviewPanel.setBoxPosition(); } + sendViewPosition(); + } @@ -477,6 +663,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int oldX = av.getStartRes(); int oldY = av.getStartSeq(); + if (evt == null || evt.getSource() == apvscroll) + { + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + // annotationPanel.image=null; + // alabels.image=null; + // alabels.repaint(); + // annotationPanel.repaint(); + } if (evt == null || evt.getSource() == hscroll) { int x = hscroll.getValue(); @@ -537,8 +732,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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) { @@ -547,7 +747,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (updateOverview) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + .getStructureSelectionManager(av.applet).sequenceColoursChanged(this); if (overviewPanel != null) { @@ -566,16 +766,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener invalidate(); Dimension d = idPanel.idCanvas.getSize(); idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); - annotationSpaceFillerHolder.setSize(d.width, - annotationPanel.getSize().height); - - alabels.setSize(d.width, annotationPanel.getSize().height); - + 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; } @@ -586,7 +782,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (canvasWidth > 0) { int max = maxwidth / canvasWidth; - vscroll.setMaximum(max); + vscroll.setMaximum(1 + max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); } @@ -642,12 +838,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener BorderLayout borderLayout2 = new BorderLayout(); + Panel annotationPanelHolder = new Panel(); + + protected Scrollbar apvscroll = new Scrollbar(); + + BorderLayout borderLayout12 = new BorderLayout(); + private void jbInit() throws Exception { // idPanelHolder.setPreferredSize(new Dimension(70, 10)); this.setLayout(borderLayout7); - // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); + //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); sequenceHolderPanel.setLayout(borderLayout3); seqPanelHolder.setLayout(borderLayout1); scalePanelHolder.setBackground(Color.white); @@ -666,7 +868,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener hscroll.setOrientation(Scrollbar.HORIZONTAL); hscrollHolder.setLayout(borderLayout10); hscrollFillerPanel.setBackground(Color.white); + apvscroll.setOrientation(Scrollbar.VERTICAL); + apvscroll.setVisible(true); + apvscroll.addAdjustmentListener(this); + annotationPanelHolder.setBackground(Color.white); + annotationPanelHolder.setLayout(borderLayout12); + annotationPanelHolder.add(apvscroll, BorderLayout.EAST); // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10)); hscrollHolder.setBackground(Color.white); @@ -688,4 +896,94 @@ public class AlignmentPanel extends Panel implements AdjustmentListener this.add(sequenceHolderPanel, BorderLayout.CENTER); } + /** + * hides or shows dynamic annotation rows based on groups and av state flags + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + public void updateAnnotation(boolean applyGlobalSettings) + { + // TODO: this should be merged with other annotation update stuff - that + // sits on AlignViewport + boolean updateCalcs = false; + boolean conv = av.isShowGroupConservation(); + boolean cons = av.isShowGroupConsensus(); + boolean showprf = av.isShowSequenceLogo(); + boolean showConsHist = av.isShowConsensusHistogram(); + + boolean sortg = true; + + // remove old automatic annotation + // add any new annotation + + ; // OrderedBy(av.alignment.getSequencesArray()); + // intersect alignment annotation with alignment groups + + AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); + Hashtable oldrfs = new Hashtable(); + if (aan != null) + { + 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.getAlignment().deleteAnnotation(aan[an]); + aan[an] = null; + } + } + } + if (av.getAlignment().getGroups()!= null) + { + for (SequenceGroup sg:av.getAlignment().getGroups()) + { + updateCalcs = false; + if (applyGlobalSettings || !oldrfs.containsKey(sg)) + { + // set defaults for this group's conservation/consensus + sg.setshowSequenceLogo(showprf); + sg.setShowConsensusHistogram(showConsHist); + } + if (conv) + { + updateCalcs = true; + av.getAlignment().addAnnotation(sg.getConservationRow(), 0); + } + if (cons) + { + updateCalcs = true; + av.getAlignment().addAnnotation(sg.getConsensus(), 0); + } + // refresh the annotation rows + if (updateCalcs) + { + sg.recalcConservation(); + } + } + } + oldrfs.clear(); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + 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(); + } + }