X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b7028ac1db9b1a30f4de3beda4e6451b11f2490e;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=750e82372157b0ee5d63d88836ebb1ce8f397b5d;hpb=a28784f8c598dbb91e41df691c86b282fe7174c4;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 750e823..b7028ac --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * 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, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -27,20 +27,22 @@ 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; @@ -179,8 +181,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AlignmentI al = av.getAlignment(); int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth - / 3)); + int maxwidth = Math.max(20, + Math.min(afwidth - 200, (int) 2 * afwidth / 3)); int i = 0; int idWidth = 0; String id; @@ -223,10 +225,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Highlight the given results on the alignment. * - * @param results - * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { @@ -271,19 +271,16 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 + + int[] r=results.getResults(seq, 0, av.alignment.getWidth()); if (r == null) { return false; } int start = r[0]; int end = r[1]; - // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // DEBUG + // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // + // DEBUG if (start < 0) { return false; @@ -292,6 +289,19 @@ 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.colSel.isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } if (!av.wrapAlignment) { if ((startv = av.getStartRes()) >= start) @@ -316,11 +326,11 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel != null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } - paintAlignment(!redrawOverview); + paintAlignment(redrawOverview); return true; } @@ -358,10 +368,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * - * @param b - * DOCUMENT ME! + * @param b Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -373,6 +382,10 @@ 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 @@ -381,9 +394,17 @@ 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; @@ -392,17 +413,20 @@ 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(); } /** @@ -500,12 +524,12 @@ 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) { @@ -577,9 +601,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int x = hscroll.getValue(); av.setStartRes(x); - av - .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av - .getCharWidth())) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -662,8 +684,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -859,8 +880,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av - .getCharHeight()); + pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + av.getCharHeight()); pg.setColor(currentTextColor); @@ -873,7 +894,9 @@ public class AlignmentPanel extends GAlignmentPanel implements - 4; } - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, + pg.drawString( + seq.getDisplayId(av.getShowJVSuffix()), + xPos, (((i - startSeq) * av.charHeight) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -1031,6 +1054,7 @@ 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; @@ -1296,15 +1320,14 @@ 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) { + jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); av.alignment = null; av = null; } @@ -1327,7 +1350,8 @@ public class AlignmentPanel extends GAlignmentPanel implements public void updateAnnotation(boolean applyGlobalSettings) { - // TODO: this should be merged with other annotation update stuff - that sits on AlignViewport + // 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(); @@ -1346,47 +1370,84 @@ public class AlignmentPanel extends GAlignmentPanel implements Hashtable oldrfs = new Hashtable(); if (aan != null) { - for (int an = 0; an < aan.length; an++) - { - if (aan[an].autoCalculated && aan[an].groupRef != null) + for (int an = 0; an < aan.length; an++) { - oldrfs.put(aan[an].groupRef, aan[an].groupRef); - av.alignment.deleteAnnotation(aan[an]); - aan[an] = null; + 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)) + for (int g = 0; g < gr.size(); g++) { - // set defaults for this group's conservation/consensus - sg.setIncludeAllConsSymbols(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(); + 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(); } + + @Override + public AlignmentI getAlignment() + { + return av.alignment; + } + + /** + * 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(); + } }