X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=77fc1fe51bf699d88d71c4be4aac5cae830887f3;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=f625838cd2a78ac67207d1669ad1a13355bca4ac;hpb=3e62000c93de12ce4e4a2282d8f020e21a278292;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index f625838..77fc1fe 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,19 +1,20 @@ /* - * 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 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -105,7 +106,7 @@ public class SeqCanvas extends JComponent for (int i = scalestartx; i < endx; i += 10) { int value = i; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { value = av.getColumnSelection().adjustForHiddenColumns(value); } @@ -137,22 +138,22 @@ public class SeqCanvas extends JComponent FontMetrics fm = getFontMetrics(av.getFont()); ypos += av.charHeight; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { startx = av.getColumnSelection().adjustForHiddenColumns(startx); endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } // WEST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - SequenceI seq = av.alignment.getSequenceAt(i); + SequenceI seq = av.getAlignment().getSequenceAt(i); int index = startx; int value = -1; @@ -165,7 +166,7 @@ public class SeqCanvas extends JComponent continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = av.getAlignment().getSequenceAt(i).findPosition(index); break; } @@ -196,16 +197,16 @@ public class SeqCanvas extends JComponent { ypos += av.charHeight; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { endx = av.getColumnSelection().adjustForHiddenColumns(endx); } SequenceI seq; // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - seq = av.alignment.getSequenceAt(i); + seq = av.getAlignment().getSequenceAt(i); int index = endx; int value = -1; @@ -425,9 +426,9 @@ public class SeqCanvas extends JComponent String mask = "00"; int maxWidth = 0; int tmp; - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - tmp = av.alignment.getSequenceAt(i).getEnd(); + tmp = av.getAlignment().getSequenceAt(i).getEnd(); if (tmp > maxWidth) { maxWidth = tmp; @@ -485,9 +486,9 @@ public class SeqCanvas extends JComponent int endx; int ypos = hgap; - int maxwidth = av.alignment.getWidth() - 1; + int maxwidth = av.getAlignment().getWidth() - 1; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -523,7 +524,7 @@ public class SeqCanvas extends JComponent drawNorthScale(g, startRes, endx, ypos); } - if (av.hasHiddenColumns && av.showHiddenMarkers) + if (av.hasHiddenColumns() && av.showHiddenMarkers) { g.setColor(Color.blue); int res; @@ -572,7 +573,8 @@ public class SeqCanvas extends JComponent annotations = new AnnotationPanel(av); } - annotations.drawComponent((Graphics2D) g, startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, (Graphics2D) g, + -1, startRes, endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); @@ -620,7 +622,7 @@ public class SeqCanvas extends JComponent void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { - if (!av.hasHiddenColumns) + if (!av.hasHiddenColumns()) { draw(g1, startRes, endRes, startSeq, endSeq, offset); } @@ -690,14 +692,14 @@ public class SeqCanvas extends JComponent // /////////////////////////// for (int i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); + nextSeq = av.getAlignment().getSequenceAt(i); if (nextSeq == null) { // occasionally, a race condition occurs such that the alignment row is // empty continue; } - sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * av.charHeight)); if (av.showSequenceFeatures) @@ -734,7 +736,7 @@ public class SeqCanvas extends JComponent } if (av.getSelectionGroup() != null - || av.alignment.getGroups().size() > 0) + || av.getAlignment().getGroups().size() > 0) { drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); } @@ -757,9 +759,9 @@ public class SeqCanvas extends JComponent int groupIndex = -1; int visWidth = (endRes - startRes + 1) * av.charWidth; - if ((group == null) && (av.alignment.getGroups().size() > 0)) + if ((group == null) && (av.getAlignment().getGroups().size() > 0)) { - group = (SequenceGroup) av.alignment.getGroups().elementAt(0); + group = (SequenceGroup) av.getAlignment().getGroups().get(0); groupIndex = 0; } @@ -786,11 +788,11 @@ public class SeqCanvas extends JComponent if ((sx <= (endRes - startRes) * av.charWidth) && group.getSequences(null).contains( - av.alignment.getSequenceAt(i))) + av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) && !group.getSequences(null).contains( - av.alignment.getSequenceAt(i + 1))) + av.getAlignment().getSequenceAt(i + 1))) { bottom = sy + av.charHeight; } @@ -799,7 +801,7 @@ public class SeqCanvas extends JComponent { if (((top == -1) && (i == 0)) || !group.getSequences(null).contains( - av.alignment.getSequenceAt(i - 1))) + av.getAlignment().getSequenceAt(i - 1))) { top = sy; } @@ -915,15 +917,15 @@ public class SeqCanvas extends JComponent g.setStroke(new BasicStroke()); - if (groupIndex >= av.alignment.getGroups().size()) + if (groupIndex >= av.getAlignment().getGroups().size()) { break; } - group = (SequenceGroup) av.alignment.getGroups().elementAt( - groupIndex); + group = (SequenceGroup) av.getAlignment().getGroups() + .get(groupIndex); - } while (groupIndex < av.alignment.getGroups().size()); + } while (groupIndex < av.getAlignment().getGroups().size()); }