-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class ScalePanel\r
- extends Panel\r
-{\r
-\r
- protected int offy = 4;\r
- public int width;\r
-\r
- protected AlignViewport av;\r
- AlignmentPanel ap;\r
-\r
- boolean stretchingGroup = false;\r
-\r
- public ScalePanel(AlignViewport av, AlignmentPanel ap)\r
- {\r
- setLayout(null);\r
- this.av = av;\r
- this.ap = ap;\r
-\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- doMouseReleased(evt);\r
- }\r
-\r
- });\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- doMouseDragged(evt);\r
- }\r
- });\r
-\r
- }\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int res = x / av.getCharWidth() + av.getStartRes();\r
- SequenceGroup sg = null;\r
-\r
- if (av.getColumnSelection().contains(res))\r
- {\r
- av.getColumnSelection().removeElement(res);\r
- }\r
- else\r
- {\r
- av.getColumnSelection().addElement(res);\r
-\r
- sg = new SequenceGroup();\r
- for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
- {\r
- sg.addSequence(av.alignment.getSequenceAt(i), false);\r
- }\r
-\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
-\r
- ap.annotationPanel.addEditableColumn(res);\r
- }\r
- av.setSelectionGroup(sg);\r
- ap.repaint();\r
- }\r
-\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- if (!stretchingGroup)\r
- {\r
- return;\r
- }\r
-\r
- int x = evt.getX();\r
- int res = x / av.getCharWidth() + av.getStartRes();\r
-\r
- if(res> av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth()-1;\r
- }\r
-\r
- if (!av.getColumnSelection().contains(res))\r
- {\r
- av.getColumnSelection().addElement(res);\r
- }\r
-\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- if (res > sg.getStartRes())\r
- {\r
- sg.setEndRes(res);\r
- }\r
- else if (res < sg.getStartRes())\r
- {\r
- sg.setStartRes(res);\r
- }\r
-\r
- stretchingGroup = false;\r
- ap.repaint();\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int res = x / av.getCharWidth() + av.getStartRes();\r
-\r
- if(res> av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth()-1;\r
- }\r
-\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if (sg != null)\r
- {\r
- stretchingGroup = true;\r
- if (res > sg.getStartRes())\r
- {\r
- sg.setEndRes(res);\r
- }\r
- else if (res < sg.getStartRes())\r
- {\r
- sg.setStartRes(res);\r
- }\r
-\r
- ap.annotationPanel.addEditableColumn(res);\r
- ap.repaint();\r
- }\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,\r
- getSize().height);\r
- }\r
-\r
-// scalewidth will normally be screenwidth,\r
- public void drawScale(Graphics gg, int startx, int endx, int width,\r
- int height)\r
- {\r
- gg.setFont(av.getFont());\r
-\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, width, height);\r
- gg.setColor(Color.black);\r
-\r
- //Fill the selected columns\r
- ColumnSelection cs = av.getColumnSelection();\r
- gg.setColor(new Color(220, 0, 0));\r
- for (int i = 0; i < cs.size(); i++)\r
- {\r
- int sel = cs.columnAt(i);\r
- if (sel >= startx && sel <= endx)\r
- {\r
- gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,\r
- getSize().height);\r
- }\r
- }\r
-\r
- // Draw the scale numbers\r
- gg.setColor(Color.black);\r
- int scalestartx = (startx / 10) * 10;\r
-\r
- FontMetrics fm = gg.getFontMetrics(av.getFont());\r
- int y = av.charHeight - fm.getDescent();\r
-\r
- if (scalestartx % 10 == 0)\r
- {\r
- scalestartx += 5;\r
- }\r
-\r
- for (int i = scalestartx; i < endx; i += 5)\r
- {\r
- if (i % 10 == 0)\r
- {\r
- gg.drawString(String.valueOf(i), (i - startx - 1) * av.charWidth, y);\r
- gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y + 2,\r
- (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y + fm.getDescent() * 2);\r
- }\r
- else\r
- {\r
- gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y + fm.getDescent(),\r
- (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),\r
- y + fm.getDescent() * 2);\r
- }\r
-\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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 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/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class ScalePanel extends Panel implements MouseMotionListener,
+ MouseListener
+{
+
+ protected int offy = 4;
+
+ public int width;
+
+ protected AlignViewport av;
+
+ AlignmentPanel ap;
+
+ boolean stretchingGroup = false;
+
+ int min; // used by mouseDragged to see if user
+
+ int max; // used by mouseDragged to see if user
+
+ boolean mouseDragging = false;
+
+ int[] reveal;
+
+ public ScalePanel(AlignViewport av, AlignmentPanel ap)
+ {
+ setLayout(null);
+ this.av = av;
+ this.ap = ap;
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ final int res;
+
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(x);
+ }
+ else
+ {
+ res = x;
+ }
+
+ min = res;
+ max = res;
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ PopupMenu pop = new PopupMenu();
+ if (reveal != null)
+ {
+ MenuItem item = new MenuItem("Reveal");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ av.showColumn(reveal[0]);
+ reveal = null;
+ ap.paintAlignment(true);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ pop.add(item);
+
+ if (av.getColumnSelection().getHiddenColumns().size() > 1)
+ {
+ item = new MenuItem("Reveal All");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ av.showAllHiddenColumns();
+ reveal = null;
+ ap.paintAlignment(true);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ pop.add(item);
+ }
+ this.add(pop);
+ pop.show(this, evt.getX(), evt.getY());
+ }
+ else if (av.getColumnSelection().contains(res))
+ {
+ MenuItem item = new MenuItem("Hide Columns");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ av.hideColumns(res, res);
+ if (av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() == av.alignment
+ .getHeight())
+ {
+ av.setSelectionGroup(null);
+ }
+
+ ap.paintAlignment(true);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ pop.add(item);
+ this.add(pop);
+ pop.show(this, evt.getX(), evt.getY());
+ }
+ }
+ else
+ // LEFT MOUSE TO SELECT
+ {
+ if (!evt.isControlDown() && !evt.isShiftDown())
+ {
+ av.getColumnSelection().clear();
+ }
+
+ av.getColumnSelection().addElement(res);
+ SequenceGroup sg = new SequenceGroup();
+ for (int i = 0; i < av.alignment.getSequences().size(); i++)
+ {
+ sg.addSequence(av.alignment.getSequenceAt(i), false);
+ }
+
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ av.setSelectionGroup(sg);
+
+ if (evt.isShiftDown())
+ {
+ int min = Math.min(av.getColumnSelection().getMin(), res);
+ int max = Math.max(av.getColumnSelection().getMax(), res);
+ for (int i = min; i < max; i++)
+ {
+ av.getColumnSelection().addElement(i);
+ }
+ sg.setStartRes(min);
+ sg.setEndRes(max);
+ }
+ }
+
+ ap.paintAlignment(true);
+ av.sendSelection();
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+ if (res > av.alignment.getWidth())
+ {
+ res = av.alignment.getWidth() - 1;
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
+
+ if (!stretchingGroup)
+ {
+ ap.paintAlignment(false);
+
+ return;
+ }
+
+ SequenceGroup sg = av.getSelectionGroup();
+
+ if (res > sg.getStartRes())
+ {
+ sg.setEndRes(res);
+ }
+ else if (res < sg.getStartRes())
+ {
+ sg.setStartRes(res);
+ }
+
+ stretchingGroup = false;
+ ap.paintAlignment(false);
+ av.sendSelection();
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ mouseDragging = true;
+
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
+
+ if (res > av.alignment.getWidth())
+ {
+ res = av.alignment.getWidth() - 1;
+ }
+
+ if (res < min)
+ {
+ min = res;
+ }
+
+ if (res > max)
+ {
+ max = res;
+ }
+
+ SequenceGroup sg = av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ stretchingGroup = true;
+
+ if (!av.getColumnSelection().contains(res))
+ {
+ av.getColumnSelection().addElement(res);
+ }
+
+ if (res > sg.getStartRes())
+ {
+ sg.setEndRes(res);
+ }
+ if (res < sg.getStartRes())
+ {
+ sg.setStartRes(res);
+ }
+
+ int col;
+ for (int i = min; i <= max; i++)
+ {
+ col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+ if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
+ {
+ av.getColumnSelection().removeElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(col);
+ }
+ }
+
+ ap.paintAlignment(false);
+ }
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (mouseDragging)
+ {
+ ap.seqPanel.scrollCanvas(null);
+ }
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ if (mouseDragging)
+ {
+ ap.seqPanel.scrollCanvas(evt);
+ }
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (!av.hasHiddenColumns)
+ {
+ return;
+ }
+
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+ reveal = null;
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(i);
+ if (res + 1 == region[0] || res - 1 == region[1])
+ {
+ reveal = region;
+ break;
+ }
+ }
+
+ repaint();
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+ drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+ getSize().height);
+ }
+
+ // scalewidth will normally be screenwidth,
+ public void drawScale(Graphics gg, int startx, int endx, int width,
+ int height)
+ {
+ gg.setFont(av.getFont());
+
+ // Fill in the background
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, width, height);
+ gg.setColor(Color.black);
+
+ // Fill the selected columns
+ ColumnSelection cs = av.getColumnSelection();
+ gg.setColor(new Color(220, 0, 0));
+
+ for (int i = 0; i < cs.size(); i++)
+ {
+ int sel = cs.columnAt(i);
+ if (av.hasHiddenColumns)
+ {
+ sel = av.getColumnSelection().findColumnPosition(sel);
+ }
+
+ if ((sel >= startx) && (sel <= endx))
+ {
+ gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+ getSize().height);
+ }
+ }
+
+ // Draw the scale numbers
+ gg.setColor(Color.black);
+
+ int scalestartx = (startx / 10) * 10;
+
+ FontMetrics fm = gg.getFontMetrics(av.getFont());
+ int y = av.charHeight - fm.getDescent();
+
+ if ((scalestartx % 10) == 0)
+ {
+ scalestartx += 5;
+ }
+
+ String string;
+ int maxX = 0;
+
+ for (int i = scalestartx; i < endx; i += 5)
+ {
+ if ((i % 10) == 0)
+ {
+ string = String.valueOf(av.getColumnSelection()
+ .adjustForHiddenColumns(i));
+ if ((i - startx - 1) * av.charWidth > maxX)
+ {
+ gg.drawString(string, (i - startx - 1) * av.charWidth, y);
+ maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+ }
+
+ gg.drawLine(
+ (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ y + 2,
+ (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ y + (fm.getDescent() * 2));
+
+ }
+ else
+ {
+ gg.drawLine(
+ (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ y + fm.getDescent(),
+ (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+ y + (fm.getDescent() * 2));
+ }
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ gg.setColor(Color.blue);
+ int res;
+ if (av.getShowHiddenMarkers())
+ {
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+ .size(); i++)
+ {
+
+ res = av.getColumnSelection().findHiddenRegionPosition(i)
+ - startx;
+
+ if (res < 0 || res > endx - scalestartx)
+ {
+ continue;
+ }
+
+ gg.fillPolygon(new int[]
+ { res * av.charWidth - av.charHeight / 4,
+ res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ new int[]
+ { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
+ 3);
+
+ }
+ }
+
+ if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+ {
+ gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+ }
+ }
+
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff