-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class OverviewPanel\r
- extends JPanel implements Runnable\r
-{\r
- BufferedImage miniMe;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- float scalew = 1f;\r
- float scaleh = 1f;\r
- int width;\r
- int sequencesHeight;\r
- int graphHeight = 20;\r
- int boxX = -1;\r
- int boxY = -1;\r
- int boxWidth = -1;\r
- int boxHeight = -1;\r
- boolean resizing = false;\r
-\r
- // Can set different properties in this seqCanvas than\r
- // main visible SeqCanvas\r
- SequenceRenderer sr;\r
- FeatureRenderer fr;\r
-\r
- /**\r
- * Creates a new OverviewPanel object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- */\r
- public OverviewPanel(AlignmentPanel ap)\r
- {\r
- this.av = ap.av;\r
- this.ap = ap;\r
- setLayout(null);\r
-\r
- sr = new SequenceRenderer(av);\r
- sr.renderGaps = false;\r
- sr.forOverview = true;\r
- fr = new FeatureRenderer(ap);\r
-\r
- // scale the initial size of overviewpanel to shape of alignment\r
- float initialScale = (float) av.alignment.getWidth() /\r
- (float) av.alignment.getHeight();\r
-\r
- if (av.conservation == null)\r
- {\r
- graphHeight = 0;\r
- }\r
-\r
- if (av.alignment.getWidth() > av.alignment.getHeight())\r
- {\r
- // wider\r
- width = 400;\r
- sequencesHeight = (int) (400f / initialScale);\r
- if (sequencesHeight < 40)\r
- {\r
- sequencesHeight = 40;\r
- }\r
- }\r
- else\r
- {\r
- // taller\r
- width = (int) (400f * initialScale);\r
- sequencesHeight = 300;\r
-\r
- if (width < 120)\r
- {\r
- width = 120;\r
- }\r
- }\r
-\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if ( (getWidth() != width) ||\r
- (getHeight() != (sequencesHeight + graphHeight)))\r
- {\r
- updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if (!av.wrapAlignment)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- }\r
- }\r
- });\r
-\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if (!av.wrapAlignment)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- }\r
- }\r
- });\r
-\r
- updateOverviewImage();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void checkValid()\r
- {\r
- if (boxY < 0)\r
- {\r
- boxY = 0;\r
- }\r
-\r
- if (boxY > (sequencesHeight - boxHeight))\r
- {\r
- boxY = sequencesHeight - boxHeight + 1;\r
- }\r
-\r
- if (boxX < 0)\r
- {\r
- boxX = 0;\r
- }\r
-\r
- if (boxX > (width - boxWidth))\r
- {\r
- if (av.hasHiddenColumns)\r
- {\r
- //Try smallest possible box\r
- boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
- av.getCharWidth() * scalew);\r
- }\r
- boxX = width - boxWidth;\r
- }\r
-\r
- int col = (int) (boxX / scalew / av.getCharWidth());\r
- int row = (int) (boxY / scaleh / av.getCharHeight());\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- if (!av.getColumnSelection().isVisible(col))\r
- {\r
- return;\r
- }\r
-\r
- col = av.getColumnSelection().findColumnPosition(col);\r
- }\r
-\r
- if (av.hasHiddenRows)\r
- {\r
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
- }\r
-\r
- ap.setScrollValues(col, row);\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateOverviewImage()\r
- {\r
- if (resizing)\r
- {\r
- resizeAgain = true;\r
- return;\r
- }\r
-\r
- resizing = true;\r
-\r
- if ( (getWidth() > 0) && (getHeight() > 0))\r
- {\r
- width = getWidth();\r
- sequencesHeight = getHeight() - graphHeight;\r
- }\r
-\r
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
-\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- repaint();\r
- }\r
-\r
- // This is set true if the user resizes whilst\r
- // the overview is being calculated\r
- boolean resizeAgain = false;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- miniMe = null;\r
-\r
- if (av.showSequenceFeatures)\r
- {\r
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
- }\r
-\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight()\r
- + av.alignment.getHiddenSequences().getSize();\r
-\r
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
-\r
- int fullsizeWidth = alwidth * av.getCharWidth();\r
- int fullsizeHeight = alheight * av.getCharHeight();\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- miniMe = new BufferedImage(width, sequencesHeight + graphHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
-\r
- Graphics mg = miniMe.getGraphics();\r
- mg.setColor(Color.orange);\r
- mg.fillRect(0, 0, width, miniMe.getHeight());\r
-\r
- float sampleCol = (float) alwidth / (float) width;\r
- float sampleRow = (float) alheight / (float) sequencesHeight;\r
-\r
- int lastcol = -1, lastrow = -1;\r
- int color = Color.white.getRGB();\r
- int row, col;\r
- jalview.datamodel.SequenceI seq;\r
- boolean hiddenRow = false;\r
- for (row = 0; row < sequencesHeight; row++)\r
- {\r
- if ( (int) (row * sampleRow) == lastrow)\r
- {\r
- //No need to recalculate the colours,\r
- //Just copy from the row above\r
- for (col = 0; col < width; col++)\r
- {\r
- miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));\r
- }\r
- continue;\r
- }\r
-\r
- lastrow = (int) (row * sampleRow);\r
-\r
- hiddenRow = false;\r
- if (av.hasHiddenRows)\r
- {\r
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
- if (seq == null)\r
- {\r
- int index =\r
- av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(\r
- lastrow);\r
-\r
- seq = av.alignment.getSequenceAt(index);\r
- }\r
- else\r
- {\r
- hiddenRow = true;\r
- }\r
- }\r
- else\r
- {\r
- seq = av.alignment.getSequenceAt(lastrow);\r
- }\r
-\r
- if (seq == null)\r
- {\r
- System.out.println(lastrow + " null");\r
- continue;\r
- }\r
-\r
- for (col = 0; col < width; col++)\r
- {\r
- if ( (int) (col * sampleCol) == lastcol &&\r
- (int) (row * sampleRow) == lastrow)\r
- {\r
- miniMe.setRGB(col, row, color);\r
- continue;\r
- }\r
-\r
- lastcol = (int) (col * sampleCol);\r
-\r
- if (seq.getLength() > lastcol)\r
- {\r
- color = sr.getResidueBoxColour(\r
- seq, lastcol).getRGB();\r
-\r
- if (av.showSequenceFeatures)\r
- {\r
- color = fr.findFeatureColour(color, seq, lastcol);\r
- }\r
- }\r
- else\r
- {\r
- color = -1; //White\r
- }\r
-\r
- if (hiddenRow ||\r
- (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
- {\r
- color = new Color(color).darker().darker().getRGB();\r
- }\r
-\r
- miniMe.setRGB(col, row, color);\r
-\r
- }\r
- }\r
-\r
- if (av.conservation != null)\r
- {\r
- for (col = 0; col < width; col++)\r
- {\r
- lastcol = (int) (col * sampleCol);\r
- {\r
- mg.translate(col, sequencesHeight);\r
- ap.annotationPanel.drawGraph(mg, av.conservation,\r
- (int) (sampleCol) + 1,\r
- graphHeight,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol) + 1);\r
- mg.translate( -col, -sequencesHeight);\r
- }\r
- }\r
- }\r
- System.gc();\r
-\r
- resizing = false;\r
-\r
- setBoxPosition();\r
-\r
- if (resizeAgain)\r
- {\r
- resizeAgain = false;\r
- updateOverviewImage();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void setBoxPosition()\r
- {\r
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
- int fullsizeHeight = (av.alignment.getHeight()\r
- + av.alignment.getHiddenSequences().getSize()) *\r
- av.getCharHeight();\r
-\r
- int startRes = av.getStartRes();\r
- int endRes = av.getEndRes();\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);\r
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
- }\r
-\r
- int startSeq = av.startSeq;\r
- int endSeq = av.endSeq;\r
-\r
- if (av.hasHiddenRows)\r
- {\r
- startSeq =\r
- av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
-\r
- endSeq =\r
- av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
-\r
- }\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- boxX = (int) (startRes * av.getCharWidth() * scalew);\r
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
- }\r
- else\r
- {\r
- boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
- }\r
-\r
- boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);\r
-\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\r
- if(resizing)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(),getHeight());\r
- }\r
- else if (miniMe != null)\r
- {\r
- g.drawImage(miniMe, 0, 0, this);\r
- }\r
-\r
- g.setColor(Color.red);\r
- g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.renderer.AnnotationRenderer;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
+{
+ BufferedImage miniMe;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ final AnnotationRenderer renderer = new AnnotationRenderer();
+
+ float scalew = 1f;
+
+ float scaleh = 1f;
+
+ int width;
+
+ int sequencesHeight;
+
+ int graphHeight = 20;
+
+ int boxX = -1;
+
+ int boxY = -1;
+
+ int boxWidth = -1;
+
+ int boxHeight = -1;
+
+ boolean resizing = false;
+
+ // Can set different properties in this seqCanvas than
+ // main visible SeqCanvas
+ SequenceRenderer sr;
+
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ /**
+ * Creates a new OverviewPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public OverviewPanel(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+ setLayout(null);
+
+ sr = new SequenceRenderer(av);
+ sr.renderGaps = false;
+ sr.forOverview = true;
+ fr = new FeatureRenderer(ap);
+
+ // scale the initial size of overviewpanel to shape of alignment
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
+
+ if (av.getAlignmentConservationAnnotation() == null)
+ {
+ graphHeight = 0;
+ }
+
+ if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
+ {
+ // wider
+ width = 400;
+ sequencesHeight = (int) (400f / initialScale);
+ if (sequencesHeight < 40)
+ {
+ sequencesHeight = 40;
+ }
+ }
+ else
+ {
+ // taller
+ width = (int) (400f * initialScale);
+ sequencesHeight = 300;
+
+ if (width < 120)
+ {
+ width = 120;
+ }
+ }
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ if ((getWidth() != width)
+ || (getHeight() != (sequencesHeight + graphHeight)))
+ {
+ updateOverviewImage();
+ }
+ }
+ });
+
+ addMouseMotionListener(new MouseMotionAdapter()
+ {
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (!av.getWrapAlignment())
+ {
+ // TODO: feature: jv2.5 detect shift drag and update selection from
+ // it.
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+ }
+ });
+
+ addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (!av.getWrapAlignment())
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+ }
+ });
+
+ updateOverviewImage();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void checkValid()
+ {
+ if (boxY < 0)
+ {
+ boxY = 0;
+ }
+
+ if (boxY > (sequencesHeight - boxHeight))
+ {
+ boxY = sequencesHeight - boxHeight + 1;
+ }
+
+ if (boxX < 0)
+ {
+ boxX = 0;
+ }
+
+ if (boxX > (width - boxWidth))
+ {
+ if (av.hasHiddenColumns())
+ {
+ // Try smallest possible box
+ boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
+ }
+ boxX = width - boxWidth;
+ }
+
+ int col = (int) (boxX / scalew / av.getCharWidth());
+ int row = (int) (boxY / scaleh / av.getCharHeight());
+
+ if (av.hasHiddenColumns())
+ {
+ if (!av.getColumnSelection().isVisible(col))
+ {
+ return;
+ }
+
+ col = av.getColumnSelection().findColumnPosition(col);
+ }
+
+ if (av.hasHiddenRows())
+ {
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
+ }
+
+ ap.setScrollValues(col, row);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateOverviewImage()
+ {
+ if (resizing)
+ {
+ resizeAgain = true;
+ return;
+ }
+
+ resizing = true;
+
+ if ((getWidth() > 0) && (getHeight() > 0))
+ {
+ width = getWidth();
+ sequencesHeight = getHeight() - graphHeight;
+ }
+
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+ Thread thread = new Thread(this);
+ thread.start();
+ repaint();
+ }
+
+ // This is set true if the user resizes whilst
+ // the overview is being calculated
+ boolean resizeAgain = false;
+
+ /**
+ * DOCUMENT ME!
+ */
+ @Override
+ public void run()
+ {
+ miniMe = null;
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
+
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+ int fullsizeWidth = alwidth * av.getCharWidth();
+ int fullsizeHeight = alheight * av.getCharHeight();
+
+ scalew = (float) width / (float) fullsizeWidth;
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+ miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+ BufferedImage.TYPE_INT_RGB);
+
+ Graphics mg = miniMe.getGraphics();
+ mg.setColor(Color.orange);
+ mg.fillRect(0, 0, width, miniMe.getHeight());
+
+ float sampleCol = (float) alwidth / (float) width;
+ float sampleRow = (float) alheight / (float) sequencesHeight;
+
+ int lastcol = -1, lastrow = -1;
+ int color = Color.white.getRGB();
+ int row, col;
+ jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
+ boolean hiddenRow = false;
+ for (row = 0; row < sequencesHeight; row++)
+ {
+ if ((int) (row * sampleRow) == lastrow)
+ {
+ // No need to recalculate the colours,
+ // Just copy from the row above
+ for (col = 0; col < width; col++)
+ {
+ miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
+ }
+ continue;
+ }
+
+ lastrow = (int) (row * sampleRow);
+
+ hiddenRow = false;
+ if (hasHiddenRows)
+ {
+ seq = av.getAlignment().getHiddenSequences()
+ .getHiddenSequence(lastrow);
+ if (seq == null)
+ {
+ int index = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(lastrow);
+
+ seq = av.getAlignment().getSequenceAt(index);
+ }
+ else
+ {
+ hiddenRow = true;
+ }
+ }
+ else
+ {
+ seq = av.getAlignment().getSequenceAt(lastrow);
+ }
+
+ if (seq == null)
+ {
+ System.out.println(lastrow + " null");
+ continue;
+ }
+
+ for (col = 0; col < width; col++)
+ {
+ if ((int) (col * sampleCol) == lastcol
+ && (int) (row * sampleRow) == lastrow)
+ {
+ miniMe.setRGB(col, row, color);
+ continue;
+ }
+
+ lastcol = (int) (col * sampleCol);
+
+ if (seq.getLength() > lastcol)
+ {
+ color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+ if (av.isShowSequenceFeatures())
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
+ }
+ else
+ {
+ color = -1; // White
+ }
+
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
+ {
+ color = new Color(color).darker().darker().getRGB();
+ }
+
+ miniMe.setRGB(col, row, color);
+
+ }
+ }
+
+ if (av.getAlignmentConservationAnnotation() != null)
+ {
+ renderer.updateFromAlignViewport(av);
+ for (col = 0; col < width; col++)
+ {
+ lastcol = (int) (col * sampleCol);
+ {
+ mg.translate(col, sequencesHeight);
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
+ (int) (sampleCol) + 1, graphHeight,
+ (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+ mg.translate(-col, -sequencesHeight);
+ }
+ }
+ }
+ System.gc();
+
+ resizing = false;
+
+ setBoxPosition();
+
+ if (resizeAgain)
+ {
+ resizeAgain = false;
+ updateOverviewImage();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setBoxPosition()
+ {
+ 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())
+ {
+ startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+ endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+ }
+
+ int startSeq = av.startSeq;
+ int endSeq = av.endSeq;
+
+ if (av.hasHiddenRows())
+ {
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
+
+ endSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(endSeq);
+
+ }
+
+ scalew = (float) width / (float) fullsizeWidth;
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+ boxX = (int) (startRes * av.getCharWidth() * scalew);
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+ if (av.hasHiddenColumns())
+ {
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ }
+ else
+ {
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ }
+
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ if (resizing)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else if (miniMe != null)
+ {
+ g.drawImage(miniMe, 0, 0, this);
+ }
+
+ g.setColor(Color.red);
+ g.drawRect(boxX, boxY, boxWidth, boxHeight);
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff