X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=b27554756c1a9d554c307d1358dd61f17727b1c3;hb=9e0de5f746594b5ccb94b548e4a1bd948ea3acdc;hp=1296829e7891545125ea4665cc0e029a70792c31;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 1296829..b275547 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. @@ -19,10 +19,13 @@ 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.*; -public class AlignmentPanel extends Panel implements AdjustmentListener +public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { public AlignViewport av; @@ -63,8 +66,9 @@ 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 +83,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener fontChanged(); setScrollValues(0, 0); + apvscroll.addAdjustmentListener(this); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -100,7 +105,6 @@ 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 +156,15 @@ 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 +178,7 @@ 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(); } @@ -224,18 +230,39 @@ 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) @@ -243,23 +270,46 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int seqIndex = av.alignment.findIndex(results); if (seqIndex == -1) { - return; + return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int[] r = results.getResults(seq, seq.getStart(), seq.getEnd()); + int[] r = results.getResults(seq, 0,av.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 didn't happen: 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.hasHiddenColumns) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!av.colSel.isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } } if (!av.wrapAlignment) { @@ -274,6 +324,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { start = 0; } + } if (seqIndex > av.alignment.getHeight() - vextent) { @@ -291,8 +342,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener scrollToWrappedVisible(start); } } - - repaint(); + if (redrawOverview && overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(redrawOverview); + return true; } void scrollToWrappedVisible(int res) @@ -321,7 +376,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationPanel.setVisible(b); + annotationPanelHolder.setVisible(b); } validate(); repaint(); @@ -338,12 +393,12 @@ 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); } @@ -418,12 +473,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener } av.setStartRes(x); - av - .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; - + if (hextent > width) { hextent = width; @@ -478,6 +532,15 @@ 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(); @@ -567,11 +630,7 @@ 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(); @@ -587,7 +646,7 @@ 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); } @@ -643,12 +702,18 @@ 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); @@ -667,7 +732,13 @@ 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); @@ -689,4 +760,141 @@ 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 + + Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); + // intersect alignment annotation with alignment groups + + AlignmentAnnotation[] aan = av.alignment.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.alignment.deleteAnnotation(aan[an]); + aan[an] = null; + } + } + } + SequenceGroup sg; + if (gr != null) + { + 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.setshowSequenceLogo(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(); + } + + /** + * 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(); + addNotify(); + repaint(); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + int height = annotationPanel.calcPanelHeight(); + if (hscroll.isVisible()) + { + height += hscroll.getPreferredSize().height; + } + int mheight = height; + // sets initial preferred height + if ((height+40) > getSize().height / 2) + { + height = getSize().height / 2; + } + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height=seqPanelHolder.getSize().height; + } + Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize(); + annotationPanel.setSize(new Dimension(d.width,height)); + alabels.setSize(e.width,height); + annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); + annotationPanelHolder.setSize(new Dimension(d.width, height)); + seqPanelHolder.setSize(d.width,d.height-height); + int s=apvscroll.getValue(); + if (s>mheight-height) + { + s = 0; + } + apvscroll.setValues(apvscroll.getValue(), height, 0, mheight); + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + } + + @Override + public AlignmentI getAlignment() + { + return av.alignment; + } + }