X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=68b3d01dfedd17f3406364401173b07940b01fdc;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=06df9f4fb909640b9579ac89599246d70cbd1ab7;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 06df9f4..68b3d01 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -1,23 +1,24 @@ /* - * 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 - * - * This program is free software; you can redistribute it and/or + * 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * 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. - * - * 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 + * 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 . */ package jalview.appletgui; +import jalview.datamodel.AlignmentI; + import java.awt.*; import java.awt.event.*; @@ -68,15 +69,15 @@ public class OverviewPanel extends Panel implements Runnable, fr.overview = true; // 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.hconsensus == null) + if (av.getSequenceConsensusHash() == null) { graphHeight = 0; } - if (av.alignment.getWidth() > av.alignment.getHeight()) + if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) { // wider width = 400; @@ -101,6 +102,7 @@ public class OverviewPanel extends Panel implements Runnable, addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { if (getSize().width != width @@ -119,22 +121,27 @@ public class OverviewPanel extends Panel implements Runnable, } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mouseMoved(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { boxX = evt.getX(); @@ -142,6 +149,7 @@ public class OverviewPanel extends Panel implements Runnable, checkValid(); } + @Override public void mouseReleased(MouseEvent evt) { boxX = evt.getX(); @@ -149,6 +157,7 @@ public class OverviewPanel extends Panel implements Runnable, checkValid(); } + @Override public void mouseDragged(MouseEvent evt) { boxX = evt.getX(); @@ -175,7 +184,7 @@ public class OverviewPanel extends Panel 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 +195,7 @@ public class OverviewPanel extends Panel 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)) { @@ -196,10 +205,10 @@ public class OverviewPanel extends Panel implements Runnable, col = av.getColumnSelection().findColumnPosition(col); } - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs( - row); + row = av.getAlignment().getHiddenSequences() + .findIndexWithoutHiddenSeqs(row); } ap.setScrollValues(col, row); @@ -241,11 +250,12 @@ public class OverviewPanel extends Panel implements Runnable, // the overview is being calculated boolean resizeAgain = false; + @Override public void run() { miniMe = null; - int alwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight(); + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight(); if (av.showSequenceFeatures) { @@ -279,6 +289,7 @@ public class OverviewPanel extends Panel implements Runnable, int row, col, sameRow = 0, sameCol = 0; jalview.datamodel.SequenceI seq; boolean hiddenRow = false; + AlignmentI alignment = av.getAlignment(); for (row = 0; row <= sequencesHeight; row++) { if ((int) (row * sampleRow) == lastrow) @@ -288,15 +299,15 @@ public class OverviewPanel extends Panel implements Runnable, } hiddenRow = false; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); + seq = alignment.getHiddenSequences().getHiddenSequence(lastrow); if (seq == null) { - int index = av.alignment.getHiddenSequences() + int index = alignment.getHiddenSequences() .findIndexWithoutHiddenSeqs(lastrow); - seq = av.alignment.getSequenceAt(index); + seq = alignment.getSequenceAt(index); } else { @@ -305,7 +316,7 @@ public class OverviewPanel extends Panel implements Runnable, } else { - seq = av.alignment.getSequenceAt(lastrow); + seq = alignment.getSequenceAt(lastrow); } for (col = 0; col < width; col++) @@ -334,7 +345,7 @@ public class OverviewPanel extends Panel implements Runnable, } if (hiddenRow - || (av.hasHiddenColumns && !av.getColumnSelection() + || (av.hasHiddenColumns() && !av.getColumnSelection() .isVisible(lastcol))) { color = color.darker().darker(); @@ -358,14 +369,16 @@ public class OverviewPanel extends Panel implements Runnable, sameRow = 1; } - if (av.conservation != null) + if (av.getAlignmentConservationAnnotation() != null) { for (col = 0; col < width; col++) { lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); - ap.annotationPanel.drawGraph(mg, av.conservation, + ap.annotationPanel.renderer.drawGraph(mg, + av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); @@ -387,15 +400,15 @@ public class OverviewPanel extends Panel 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); @@ -404,12 +417,12 @@ public class OverviewPanel extends Panel implements Runnable, int startSeq = av.startSeq; int endSeq = av.endSeq; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs( - startSeq); + startSeq = av.getAlignment().getHiddenSequences() + .adjustForHiddenSeqs(startSeq); - endSeq = av.alignment.getHiddenSequences() + endSeq = av.getAlignment().getHiddenSequences() .adjustForHiddenSeqs(endSeq); } @@ -420,7 +433,7 @@ public class OverviewPanel extends Panel 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); } @@ -434,11 +447,13 @@ public class OverviewPanel extends Panel implements Runnable, repaint(); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { Graphics og = offscreen.getGraphics();