X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=eaa3a501251888160f22220e98b25ebb348ba858;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f0031a8c5a30e3abb922b6fd99328a6ab2c7cd3e;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index f0031a8..eaa3a50 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,26 +1,35 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.awt.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.Panel; public class SeqCanvas extends Panel { @@ -79,7 +88,7 @@ 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); } @@ -98,22 +107,22 @@ 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; @@ -126,7 +135,7 @@ public class SeqCanvas extends Panel continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = av.getAlignment().getSequenceAt(i).findPosition(index); break; } @@ -145,16 +154,16 @@ 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; @@ -349,9 +358,10 @@ 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; @@ -398,9 +408,9 @@ 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; } @@ -434,7 +444,7 @@ 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; @@ -507,51 +517,52 @@ 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); } else { - java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); int screenY = 0; int blockStart = startRes; int blockEnd = endRes; - for (int i = 0; i < regions.size(); i++) + if (av.hasHiddenColumns()) { - int[] region = (int[]) regions.elementAt(i); - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) + for (int[] region : av.getColumnSelection().getHiddenColumns()) { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } - blockEnd = hideStart - 1; + blockEnd = hideStart - 1; - g1.translate(screenY * av.charWidth, 0); + g1.translate(screenY * av.charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - 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); - } + 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.translate(-screenY * av.charWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; + g1.translate(-screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + } } - if (screenY <= (endRes - startRes)) { blockEnd = blockStart + (endRes - startRes) - screenY; @@ -578,17 +589,17 @@ 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) + if (av.isShowSequenceFeatures()) { fr.drawSequence(g, nextSeq, startRes, endRes, offset + ((i - startSeq) * av.charHeight)); @@ -622,7 +633,7 @@ 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); } @@ -643,9 +654,9 @@ 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 = av.getAlignment().getGroups().get(0); groupIndex = 0; } @@ -658,7 +669,7 @@ 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++) { @@ -673,11 +684,12 @@ 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; } @@ -686,7 +698,7 @@ 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; } @@ -796,14 +808,14 @@ 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 = av.getAlignment().getGroups() + .get(groupIndex); + } while (groupIndex < av.getAlignment().getGroups().size()); } }