X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=bfbaf4d0bb8262a591714564d75ce4c7a605d0c8;hb=ff7e72d6df848ca0694d25bde0e9616e8df1d18e;hp=efefeafbada38512aa86f69d4377d8d6675873eb;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index efefeaf..bfbaf4d --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * 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. * @@ -27,20 +27,21 @@ import java.awt.event.*; import java.awt.print.*; import javax.swing.*; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; -import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable + AdjustmentListener, Printable, AlignmentViewPanel { public AlignViewport av; @@ -223,10 +224,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Highlight the given results on the alignment. * - * @param results - * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { @@ -263,20 +262,16 @@ public class AlignmentPanel extends GAlignmentPanel implements // do we need to scroll the panel? // TODO: tons of nullpointereexceptions raised here. if (results != null && results.getSize() > 0 && av != null - && av.alignment != null) + && av.getAlignment() != null) { - int seqIndex = av.alignment.findIndex(results); + int seqIndex = av.getAlignment().findIndex(results); if (seqIndex == -1) { return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - - 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 + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + + int[] r=results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; @@ -293,6 +288,19 @@ public class AlignmentPanel extends GAlignmentPanel implements { return false; } + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start==end) + { + if (!av.getColumnSelection().isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } if (!av.wrapAlignment) { if ((startv = av.getStartRes()) >= start) @@ -317,11 +325,11 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel != null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } - paintAlignment(!redrawOverview); + paintAlignment(redrawOverview); return true; } @@ -359,10 +367,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * - * @param b - * DOCUMENT ME! + * @param b Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -374,6 +381,10 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 @@ -382,9 +393,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { System.out.println("NEEDS FIXING"); } - + validateAnnotationDimensions(true); + addNotify(); + paintAlignment(true); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) { int height = annotationPanel.adjustPanelHeight(); - + if (hscroll.isVisible()) { height += hscroll.getPreferredSize().height; @@ -393,17 +412,20 @@ public class AlignmentPanel extends GAlignmentPanel implements { height = alignFrame.getHeight() / 2; } - + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height=annotationScroller.getSize().height; + } hscroll.addNotify(); - + annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), height)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); - addNotify(); - repaint(); + annotationScroller.addNotify(); } /** @@ -501,24 +523,24 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Adjust row/column scrollers to show a visible position in the alignment. * - * @param x - * DOCUMENT ME! - * @param y + * @param x visible column to scroll to * DOCUMENT ME! + * @param y visible row to scroll to + * */ public void setScrollValues(int x, int y) { // System.err.println("Scroll to "+x+","+y); - if (av == null || av.alignment == null) + if (av == null || av.getAlignment() == null) { return; } - 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); } @@ -661,8 +683,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -688,9 +709,9 @@ public class AlignmentPanel extends GAlignmentPanel implements 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; } @@ -814,7 +835,7 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = av.getAlignment().getHeight(); } - int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight; if (av.showAnnotation) { @@ -885,12 +906,12 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + if (av.showAnnotation && (endSeq == av.getAlignment().getHeight())) { pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); alabels.drawComponent((Graphics2D) pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; @@ -936,8 +957,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int idWidth = getVisibleIdWidth(); - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -963,10 +984,10 @@ public class AlignmentPanel extends GAlignmentPanel implements do { - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { pg.setFont(idPanel.idCanvas.idfont); - SequenceI s = av.alignment.getSequenceAt(i); + SequenceI s = av.getAlignment().getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; if (av.rightAlignIds) @@ -1016,13 +1037,13 @@ public class AlignmentPanel extends GAlignmentPanel implements void makeAlignmentImage(int type, File file) { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - int height = ((av.alignment.getHeight() + 1) * av.charHeight) + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + scalePanel.getHeight(); int width = getVisibleIdWidth() + (maxwidth * av.charWidth); @@ -1032,6 +1053,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { + // TODO: JAL-244 width = alignFrame.getWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - alignFrame.getInsets().right; @@ -1123,7 +1145,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment + int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment() .getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); @@ -1136,15 +1158,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { sy = s * av.charHeight + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); + SequenceI seq = av.getAlignment().getSequenceAt(s); SequenceFeature[] features = seq.getDatasetSequence() .getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + ""); @@ -1280,8 +1302,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -1297,16 +1319,15 @@ public class AlignmentPanel extends GAlignmentPanel implements */ 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; + jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); + av.setAlignment(null); av = null; } else @@ -1335,16 +1356,17 @@ public class AlignmentPanel extends GAlignmentPanel implements boolean cons = av.isShowGroupConsensus(); boolean showprf = av.isShowSequenceLogo(); boolean showConsHist = av.isShowConsensusHistogram(); + boolean normLogo = av.isNormaliseSequenceLogo(); boolean sortg = true; // remove old automatic annotation // add any new annotation - Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); + Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().getSequencesArray()); // intersect alignment annotation with alignment groups - AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); Hashtable oldrfs = new Hashtable(); if (aan != null) { @@ -1353,7 +1375,7 @@ public class AlignmentPanel extends GAlignmentPanel implements 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; } } @@ -1370,16 +1392,17 @@ public class AlignmentPanel extends GAlignmentPanel implements // set defaults for this group's conservation/consensus sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); + sg.setNormaliseSequenceLogo(normLogo); } 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) @@ -1391,4 +1414,47 @@ public class AlignmentPanel extends GAlignmentPanel implements oldrfs.clear(); adjustAnnotationHeight(); } + + @Override + public AlignmentI getAlignment() + { + return av.getAlignment(); + } + + /** + * get the name for this view + * @return + */ + public String getViewName() + { + return av.viewName; + } + + /** + * Make/Unmake this alignment panel the current input focus + * @param b + */ + public void setSelected(boolean b) + { + try { + alignFrame.setSelected(b); + } catch (Exception ex) {}; + + if (b) + { + alignFrame.setDisplayedView(this); + } + } + + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return av.getStructureSelectionManager(); + } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } }