X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=34ef556c8a23d29e09f5a4827ef3beff4c8b2008;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=6fa4933660f523d28e92b7e097b86de9c9de6040;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 6fa4933..34ef556 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/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 2.8.1) + * 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.appletgui; @@ -78,7 +79,7 @@ public class SeqCanvas extends Panel for (int i = scalestartx; i < endx; i += 10) { int value = i; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { value = av.getColumnSelection().adjustForHiddenColumns(value); } @@ -97,22 +98,22 @@ public class SeqCanvas extends Panel { 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; @@ -125,7 +126,7 @@ public class SeqCanvas extends Panel continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = av.getAlignment().getSequenceAt(i).findPosition(index); break; } @@ -144,16 +145,16 @@ public class SeqCanvas extends Panel { 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; @@ -348,9 +349,10 @@ public class SeqCanvas extends Panel String mask = "0"; int maxWidth = 0; int tmp; - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - tmp = av.alignment.getSequenceAt(i).getEnd(); + tmp = alignment.getSequenceAt(i).getEnd(); if (tmp > maxWidth) { maxWidth = tmp; @@ -397,9 +399,9 @@ public class SeqCanvas extends Panel 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; } @@ -433,7 +435,7 @@ public class SeqCanvas extends Panel { drawNorthScale(g, startRes, endx, ypos); } - if (av.hasHiddenColumns && av.showHiddenMarkers) + if (av.hasHiddenColumns() && av.showHiddenMarkers) { g.setColor(Color.blue); int res; @@ -506,7 +508,7 @@ public class SeqCanvas extends Panel 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); } @@ -539,11 +541,9 @@ public class SeqCanvas extends Panel if (av.getShowHiddenMarkers()) { g1.setColor(Color.blue); - g1 - .drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) - * av.charWidth - 1, (endSeq - startSeq) - * av.charHeight + offset); + g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) * av.charWidth + - 1, (endSeq - startSeq) * av.charHeight + offset); } g1.translate(-screenY * av.charWidth, 0); @@ -577,14 +577,14 @@ public class SeqCanvas extends Panel // /////////////////////////// for (int i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); + nextSeq = av.getAlignment().getSequenceAt(i); if (nextSeq == null) { 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) @@ -621,7 +621,7 @@ public class SeqCanvas extends Panel } if (av.getSelectionGroup() != null - || av.alignment.getGroups().size() > 0) + || av.getAlignment().getGroups().size() > 0) { drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); } @@ -642,9 +642,9 @@ public class SeqCanvas extends Panel int ex = -1; int groupIndex = -1; - 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; } @@ -657,7 +657,7 @@ public class SeqCanvas extends Panel boolean inGroup = false; int top = -1; int bottom = -1; - int alHeight = av.alignment.getHeight() - 1; + int alHeight = av.getAlignment().getHeight() - 1; for (i = startSeq; i < endSeq; i++) { @@ -672,11 +672,12 @@ public class SeqCanvas extends Panel if ((sx <= (endRes - startRes) * av.charWidth) && group.getSequences(null).contains( - av.alignment.getSequenceAt(i))) + av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) && (i >= alHeight || !group.getSequences(null) - .contains(av.alignment.getSequenceAt(i + 1)))) + .contains( + av.getAlignment().getSequenceAt(i + 1)))) { bottom = sy + av.charHeight; } @@ -685,7 +686,7 @@ public class SeqCanvas extends Panel { if (((top == -1) && (i == 0)) || !group.getSequences(null).contains( - av.alignment.getSequenceAt(i - 1))) + av.getAlignment().getSequenceAt(i - 1))) { top = sy; } @@ -795,14 +796,14 @@ public class SeqCanvas extends Panel groupIndex++; - if (groupIndex >= av.alignment.getGroups().size()) + if (groupIndex >= av.getAlignment().getGroups().size()) { break; } - group = (SequenceGroup) av.alignment.getGroups().elementAt( - groupIndex); - } while (groupIndex < av.alignment.getGroups().size()); + group = (SequenceGroup) av.getAlignment().getGroups() + .get(groupIndex); + } while (groupIndex < av.getAlignment().getGroups().size()); } }