X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=475f0c711d1e4e54fc73547e24ea39f807eed634;hb=aa213924876640ba82e866da5a750d9cdaa816d2;hp=2426d4db11de517f70d504e9ef1b9de733d7354f;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 2426d4d..475f0c7 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,22 +1,24 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * * 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 + * 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 + * + * 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 jalview.renderer.AnnotationRenderer; + import java.awt.*; import java.awt.event.*; import java.awt.image.*; @@ -24,7 +26,7 @@ import javax.swing.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @@ -36,6 +38,7 @@ public class OverviewPanel extends JPanel implements Runnable AlignmentPanel ap; + final AnnotationRenderer renderer = new AnnotationRenderer(); float scalew = 1f; float scaleh = 1f; @@ -64,7 +67,7 @@ public class OverviewPanel extends JPanel implements Runnable /** * Creates a new OverviewPanel object. - * + * * @param ap * DOCUMENT ME! */ @@ -80,15 +83,15 @@ public class OverviewPanel extends JPanel implements Runnable fr = new FeatureRenderer(ap); // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.alignment.getWidth() - / (float) av.alignment.getHeight(); + float initialScale = (float) av.getAlignment().getWidth() + / (float) av.getAlignment().getHeight(); - if (av.conservation == null) + if (av.getAlignmentConservationAnnotation()== null) { graphHeight = 0; } - if (av.alignment.getWidth() > av.alignment.getHeight()) + if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) { // wider width = 400; @@ -112,6 +115,7 @@ public class OverviewPanel extends JPanel implements Runnable addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { if ((getWidth() != width) @@ -124,6 +128,7 @@ public class OverviewPanel extends JPanel implements Runnable addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { if (!av.wrapAlignment) @@ -139,6 +144,7 @@ public class OverviewPanel extends JPanel implements Runnable addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (!av.wrapAlignment) @@ -175,7 +181,7 @@ public class OverviewPanel extends JPanel implements Runnable if (boxX > (width - boxWidth)) { - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { // Try smallest possible box boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew); @@ -186,7 +192,7 @@ public class OverviewPanel extends JPanel implements Runnable int col = (int) (boxX / scalew / av.getCharWidth()); int row = (int) (boxY / scaleh / av.getCharHeight()); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { if (!av.getColumnSelection().isVisible(col)) { @@ -196,9 +202,9 @@ public class OverviewPanel extends JPanel implements Runnable col = av.getColumnSelection().findColumnPosition(col); } - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs( + row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs( row); } @@ -239,6 +245,7 @@ public class OverviewPanel extends JPanel implements Runnable /** * DOCUMENT ME! */ + @Override public void run() { miniMe = null; @@ -248,9 +255,9 @@ public class OverviewPanel extends JPanel implements Runnable fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); } - int alwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight() - + av.alignment.getHiddenSequences().getSize(); + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); @@ -291,15 +298,15 @@ public class OverviewPanel extends JPanel implements Runnable lastrow = (int) (row * sampleRow); hiddenRow = false; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); + seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow); if (seq == null) { - int index = av.alignment.getHiddenSequences() + int index = av.getAlignment().getHiddenSequences() .findIndexWithoutHiddenSeqs(lastrow); - seq = av.alignment.getSequenceAt(index); + seq = av.getAlignment().getSequenceAt(index); } else { @@ -308,7 +315,7 @@ public class OverviewPanel extends JPanel implements Runnable } else { - seq = av.alignment.getSequenceAt(lastrow); + seq = av.getAlignment().getSequenceAt(lastrow); } if (seq == null) @@ -343,7 +350,7 @@ public class OverviewPanel extends JPanel implements Runnable } if (hiddenRow - || (av.hasHiddenColumns && !av.getColumnSelection() + || (av.hasHiddenColumns() && !av.getColumnSelection() .isVisible(lastcol))) { color = new Color(color).darker().darker().getRGB(); @@ -354,14 +361,15 @@ public class OverviewPanel extends JPanel implements Runnable } } - if (av.conservation != null) + if (av.getAlignmentConservationAnnotation()!= null) { + renderer.updateFromAlignViewport(av); for (col = 0; col < width; col++) { lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); - ap.annotationPanel.drawGraph(mg, av.conservation, + renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); @@ -386,14 +394,14 @@ public class OverviewPanel extends JPanel implements Runnable */ public void setBoxPosition() { - int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth(); - int fullsizeHeight = (av.alignment.getHeight() + av.alignment + int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth(); + int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment() .getHiddenSequences().getSize()) * av.getCharHeight(); int startRes = av.getStartRes(); int endRes = av.getEndRes(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); @@ -402,12 +410,12 @@ public class OverviewPanel extends JPanel implements Runnable int startSeq = av.startSeq; int endSeq = av.endSeq; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs( + startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs( startSeq); - endSeq = av.alignment.getHiddenSequences() + endSeq = av.getAlignment().getHiddenSequences() .adjustForHiddenSeqs(endSeq); } @@ -418,7 +426,7 @@ public class OverviewPanel extends JPanel implements Runnable boxX = (int) (startRes * av.getCharWidth() * scalew); boxY = (int) (startSeq * av.getCharHeight() * scaleh); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); } @@ -434,10 +442,11 @@ public class OverviewPanel extends JPanel implements Runnable /** * DOCUMENT ME! - * + * * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { if (resizing)