X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=95ef295345e5171f8d1fea75f4051df812a306f0;hb=ca22857ffc5d0f1fc725dfe45cfe66057051d566;hp=3316227642a9aad5bc030820c18e4d77110a4fe8;hpb=bb24cd9d9b542bde1408eeb29a38b1d7f3f5f699;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 3316227..95ef295 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,25 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, 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 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.*; @@ -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; @@ -172,15 +174,28 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public Dimension calculateIdWidth() { + // calculate sensible default width when no preference is available + + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, + Math.min(afwidth - 200, (int) 2 * afwidth / 3)); + return calculateIdWidth(maxwidth); + } + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * @param maxwidth -1 or maximum width allowed for IdWidth + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + public Dimension calculateIdWidth(int maxwidth) + { Container c = new Container(); FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); 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 i = 0; int idWidth = 0; String id; @@ -219,14 +234,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(Math.min(maxwidth, idWidth), 12); + return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** - * DOCUMENT ME! + * Highlight the given results on the alignment. * - * @param results - * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { @@ -271,18 +284,16 @@ 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 if (start < 0) { return false; @@ -291,6 +302,19 @@ 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) @@ -315,11 +339,11 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel != null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } - paintAlignment(!redrawOverview); + paintAlignment(redrawOverview); return true; } @@ -357,10 +381,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * - * @param b - * DOCUMENT ME! + * @param b Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -372,6 +395,10 @@ 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 @@ -380,9 +407,17 @@ 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; @@ -391,16 +426,20 @@ 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(); - repaint(); + annotationScroller.addNotify(); } /** @@ -498,12 +537,12 @@ 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) { @@ -575,9 +614,7 @@ 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) @@ -660,8 +697,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -766,7 +802,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -857,8 +893,8 @@ 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); @@ -871,7 +907,9 @@ 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)); } @@ -931,7 +969,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); int maxwidth = av.alignment.getWidth(); if (av.hasHiddenColumns) @@ -1004,11 +1042,33 @@ public class AlignmentPanel extends GAlignmentPanel implements return Printable.NO_SUCH_PAGE; } } - + /** + * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings + * @return + */ int getVisibleIdWidth() { - return idPanel.getWidth() > 0 ? idPanel.getWidth() - : calculateIdWidth().width + 4; + return getVisibleIdWidth(true); + } + + /** + * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings + * @param onscreen indicate if the Id width for onscreen or offscreen display should be returned + * @return + */ + int getVisibleIdWidth(boolean onscreen) + { + // see if rendering offscreen - check preferences and calc width accordingly + if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) + { + return calculateIdWidth(-1).width+4; + } + Integer idwidth=null; + if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) { + return (idPanel.getWidth() > 0 ? idPanel.getWidth() + : calculateIdWidth().width + 4); + } + return idwidth.intValue()+4; } void makeAlignmentImage(int type, File file) @@ -1021,7 +1081,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int height = ((av.alignment.getHeight() + 1) * av.charHeight) + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); + int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); if (av.getWrapAlignment()) { @@ -1029,13 +1089,16 @@ public class AlignmentPanel extends GAlignmentPanel implements if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { + // need to obtain default alignment width and then add in any additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for offscreen idWith width = alignFrame.getWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - - alignFrame.getInsets().right; + - alignFrame.getInsets().right + - getVisibleIdWidth()+getVisibleIdWidth(false); } else { - width = seqPanel.getWidth() + getVisibleIdWidth(); + width = seqPanel.getWidth() + getVisibleIdWidth(false); } } @@ -1110,7 +1173,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS // //////////////////////////////////////////// - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -1294,15 +1357,14 @@ 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; } @@ -1320,9 +1382,19 @@ public class AlignmentPanel extends GAlignmentPanel implements */ 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 @@ -1332,36 +1404,87 @@ public class AlignmentPanel extends GAlignmentPanel implements // intersect alignment annotation with alignment groups AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); - for (int an = 0; an < aan.length; an++) + Hashtable oldrfs = new Hashtable(); + if (aan != null) { - if (aan[an].autoCalculated && aan[an].groupRef != null) + for (int an = 0; an < aan.length; an++) { - 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; - for (int g = 0; g < gr.size(); g++) + if (gr != null) { - updateCalcs = false; - sg = (SequenceGroup) gr.elementAt(g); - - if (cons) + for (int g = 0; g < gr.size(); g++) { - updateCalcs = true; - av.alignment.addAnnotation(sg.getConsensus(),0); - } - if (conv) - { - updateCalcs = true; - av.alignment.addAnnotation(sg.getConservationRow(),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(); + } }