X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=1b93f104c08c23213f6ea0773cd8e06250e6303e;hpb=f6f774a4fa6885275b9d1902a4c8d470607e3447;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 1b93f10..1906829 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; private boolean headless; + IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ @@ -155,6 +156,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av; } + public void alignmentChanged() { av.alignmentChanged(this); @@ -177,8 +179,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av - .getCharHeight() - + fm.getDescent())); + .getCharHeight() + fm.getDescent())); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; @@ -317,7 +318,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) + public boolean scrollToPosition(SearchResults searchResults, + boolean redrawOverview) { return scrollToPosition(searchResults, 0, redrawOverview, false); } @@ -337,8 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, - int verticalOffset, - boolean redrawOverview, boolean centre) + int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; // TODO: properly locate search results in view when large numbers of hidden @@ -363,8 +364,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int start = r[0]; int end = r[1]; // DEBUG -// System.err.println(this.av.viewName + " Seq : " + seqIndex -// + " Scroll to " + start + "," + end); + // System.err.println(this.av.viewName + " Seq : " + seqIndex + // + " Scroll to " + start + "," + end); /* * To centre results, scroll to positions half the visible width @@ -747,7 +748,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { int x = hscroll.getValue(); av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1); + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -844,8 +846,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); - sorter.sort(getAlignment() - .getAlignmentAnnotation(), + sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); repaint(); @@ -1063,9 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements - 4; } - pg.drawString( - seq.getDisplayId(av.getShowJVSuffix()), - xPos, + pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -1074,7 +1073,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // draw main sequence panel pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, + endSeq, 0); if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) { @@ -1176,12 +1176,14 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (labels != null) { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.getCharHeight())); + pg.translate(-3, + ypos + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos + pg.translate( + +3, + -ypos - (av.getAlignment().getHeight() * av .getCharHeight())); } @@ -1191,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, - 0); + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + totalHeight, 0); if ((pi * pheight) < totalHeight) { @@ -1250,8 +1252,8 @@ public class AlignmentPanel extends GAlignmentPanel implements if (alignFrame != null && !headless) { alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] - { type.getLabel() }), progress); + "status.saving_file", new Object[] { type.getLabel() }), + progress); } try { @@ -1312,7 +1314,9 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (alignFrame != null && !headless) { - alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); + alignFrame.setProgressBar( + MessageManager.getString("status.export_complete"), + progress); } } } @@ -1377,6 +1381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); } + public void makePNGImageMap(File imgMapFile, String imageName) { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS @@ -1414,8 +1419,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getAlignment().isNucleotide()) { triplet = ResidueProperties.nucleotideName.get(seq - .getCharAt(res) - + ""); + .getCharAt(res) + ""); } else { @@ -1437,8 +1441,7 @@ public class AlignmentPanel extends GAlignmentPanel implements text.append("