X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=efefeafbada38512aa86f69d4377d8d6675873eb;hb=cce8dd5b2737f394593b3a418c7bb1836cf55c57;hp=eaa685dc86ea638ddaa52f55182da1228d39642b;hpb=22d4d2237b099daf76bd1a2ed324763972ed91aa;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index eaa685d..efefeaf 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,31 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; import java.beans.*; import java.io.*; +import java.util.Hashtable; +import java.util.Vector; import java.awt.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; +import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; @@ -70,9 +72,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! + * DOCUMENT ME! * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -177,8 +179,8 @@ 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; @@ -224,80 +226,110 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param results - * DOCUMENT ME! + * DOCUMENT ME! */ 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 + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * * @param results */ - public void scrollToPosition(SearchResults results) { - scrollToPosition(results, true); + public boolean scrollToPosition(SearchResults results) + { + return scrollToPosition(results, true); } + /** - * scroll the view to show the position of the highlighted - * region in results (if any) + * 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) + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) + * @return false if results were not found */ - public void scrollToPosition(SearchResults results, boolean redrawOverview) { + public boolean scrollToPosition(SearchResults results, + boolean redrawOverview) + { + int startv, endv, starts, ends, width; + // TODO: properly locate search results in view when large numbers of hidden + // columns exist before highlighted region // do we need to scroll the panel? - if (results != null && results.getSize()>0) + // TODO: tons of nullpointereexceptions raised here. + if (results != null && results.getSize() > 0 && av != null + && av.alignment != null) { int seqIndex = av.alignment.findIndex(results); - if (seqIndex==-1) + if (seqIndex == -1) { - return; + return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); - if (r==null) + + 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 + if (r == null) { - return; + return false; } int start = r[0]; int end = r[1]; - if (start<0) + // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // + // DEBUG + if (start < 0) { - return; + return false; } - if (end==seq.getEnd()) + if (end == seq.getEnd()) { - return; + return false; } if (!av.wrapAlignment) { - if ((av.getStartRes() >= start) - || (av.getEndRes() <= end)) + if ((startv = av.getStartRes()) >= start) { - setScrollValues(start-1, seqIndex); - } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)) + setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), seqIndex); } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } } else { scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel!=null) + if (!redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); - } + } paintAlignment(!redrawOverview); + return true; } void scrollToWrappedVisible(int res) { int cwidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth)) + if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; @@ -319,7 +351,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param op - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -330,7 +362,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAnnotationVisible(boolean b) { @@ -370,6 +402,7 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); + addNotify(); repaint(); } @@ -377,7 +410,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param wrap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { @@ -435,7 +468,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param right - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -471,13 +504,14 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param x - * DOCUMENT ME! + * DOCUMENT ME! * @param y - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScrollValues(int x, int y) { - if (av==null || av.alignment==null) + // System.err.println("Scroll to "+x+","+y); + if (av == null || av.alignment == null) { return; } @@ -532,7 +566,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -544,9 +578,7 @@ 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) @@ -643,7 +675,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -686,16 +718,16 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pf - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -719,18 +751,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -826,8 +858,8 @@ 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); @@ -840,7 +872,9 @@ 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)); } @@ -866,18 +900,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -1256,4 +1290,105 @@ public class AlignmentPanel extends GAlignmentPanel implements return height; } + + /** + * close the panel - deregisters all listeners and nulls any references to + * alignment data. + */ + 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; + av = null; + } + else + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.warn("Closing alignment panel which is already closed."); + } + } + } + + /** + * 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(); + } }