-/*\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.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class SliderPanel extends Panel\r
- implements ActionListener,\r
- AdjustmentListener,\r
- MouseListener\r
-{\r
- AlignmentPanel ap;\r
- boolean forConservation = true;\r
- ColourSchemeI cs;\r
-\r
- static Frame conservationSlider;\r
- static Frame PIDSlider;\r
-\r
- public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,\r
- String source)\r
- {\r
- SliderPanel sp = null;\r
-\r
- if (conservationSlider == null)\r
- {\r
- sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);\r
- conservationSlider = new Frame();\r
- conservationSlider.add(sp);\r
- }\r
- else\r
- {\r
- sp = (SliderPanel) conservationSlider.getComponent(0);\r
- sp.cs = cs;\r
- }\r
-\r
- conservationSlider.setTitle("Conservation Colour Increment (" + source +\r
- ")");\r
- if (ap.av.alignment.getGroups() != null)\r
- {\r
- sp.setAllGroupsCheckEnabled(true);\r
- }\r
- else\r
- {\r
- sp.setAllGroupsCheckEnabled(false);\r
- }\r
-\r
- return sp.getValue();\r
- }\r
-\r
- public static void showConservationSlider()\r
- {\r
- try\r
- {\r
- PIDSlider.setVisible(false);\r
- PIDSlider = null;\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- if (!conservationSlider.isVisible())\r
- {\r
- jalview.bin.JalviewLite.addFrame(conservationSlider,\r
- conservationSlider.getTitle(), 420, 100);\r
- conservationSlider.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- conservationSlider = null;\r
- }\r
- });\r
-\r
- }\r
-\r
- }\r
-\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
- String source)\r
- {\r
- SliderPanel pid = null;\r
- if (PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, 50, false, cs);\r
- PIDSlider = new Frame();\r
- PIDSlider.add(pid);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel) PIDSlider.getComponent(0);\r
- pid.cs = cs;\r
- }\r
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- {\r
- pid.setAllGroupsCheckEnabled(true);\r
- }\r
- else\r
- {\r
- pid.setAllGroupsCheckEnabled(false);\r
- }\r
-\r
- return pid.getValue();\r
-\r
- }\r
-\r
- public static void showPIDSlider()\r
- {\r
- try\r
- {\r
- conservationSlider.setVisible(false);\r
- conservationSlider = null;\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- if (!PIDSlider.isVisible())\r
- {\r
- jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,\r
- 100);\r
- PIDSlider.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- PIDSlider = null;\r
- }\r
- });\r
- }\r
-\r
- }\r
-\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
- ColourSchemeI cs)\r
- {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- this.ap = ap;\r
- this.cs = cs;\r
- forConservation = forConserve;\r
- undoButton.setVisible(false);\r
- applyButton.setVisible(false);\r
- if (forConservation)\r
- {\r
- label.setText("Modify conservation visibility");\r
- slider.setMinimum(0);\r
- slider.setMaximum(50 + slider.getVisibleAmount());\r
- slider.setUnitIncrement(1);\r
- }\r
- else\r
- {\r
- label.setText("Colour residues above % occurence");\r
- slider.setMinimum(0);\r
- slider.setMaximum(100 + slider.getVisibleAmount());\r
- slider.setBlockIncrement(1);\r
- }\r
-\r
- slider.addAdjustmentListener(this);\r
- slider.addMouseListener(this);\r
-\r
- slider.setValue(value);\r
- valueField.setText(value + "");\r
- }\r
-\r
- public void valueChanged(int i)\r
- {\r
- if (cs == null)\r
- {\r
- return;\r
- }\r
-\r
- ColourSchemeI toChange = null;\r
- Vector allGroups = null;\r
- int groupIndex = 0;\r
-\r
- if (allGroupsCheck.getState())\r
- {\r
- allGroups = ap.av.alignment.getGroups();\r
- groupIndex = allGroups.size() - 1;\r
- }\r
- else\r
- {\r
- toChange = cs;\r
- }\r
-\r
- while (groupIndex > -1)\r
- {\r
- if (allGroups != null)\r
- {\r
- toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;\r
- }\r
-\r
- if (forConservation)\r
- {\r
- toChange.setConservationInc(i);\r
- }\r
- else\r
- {\r
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- groupIndex--;\r
- }\r
-\r
- ap.seqPanel.seqCanvas.repaint();\r
-\r
- }\r
-\r
- public void setAllGroupsCheckEnabled(boolean b)\r
- {\r
- allGroupsCheck.setEnabled(b);\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if(evt.getSource()==applyButton)\r
- applyButton_actionPerformed();\r
- else if(evt.getSource()==undoButton)\r
- undoButton_actionPerformed();\r
- else if(evt.getSource()==valueField)\r
- valueField_actionPerformed();\r
- }\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- valueChanged(slider.getValue());\r
- }\r
-\r
-\r
- public void valueField_actionPerformed()\r
- {\r
- try\r
- {\r
- int i = Integer.parseInt(valueField.getText());\r
- slider.setValue(i);\r
- }\r
- catch (Exception ex)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- }\r
- }\r
-\r
- public void setValue(int value)\r
- {\r
- slider.setValue(value);\r
- }\r
-\r
- public int getValue()\r
- {\r
- return Integer.parseInt(valueField.getText());\r
- }\r
-\r
- // this is used for conservation colours, PID colours and redundancy threshold\r
- protected Scrollbar slider = new Scrollbar();\r
- protected TextField valueField = new TextField();\r
- protected Label label = new Label();\r
- Panel jPanel1 = new Panel();\r
- Panel jPanel2 = new Panel();\r
- protected Button applyButton = new Button();\r
- protected Button undoButton = new Button();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- protected Checkbox allGroupsCheck = new Checkbox();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- FlowLayout flowLayout2 = new FlowLayout();\r
-\r
- private void jbInit() throws Exception {\r
- this.setLayout(borderLayout2);\r
-\r
- // slider.setMajorTickSpacing(10);\r
- // slider.setMinorTickSpacing(1);\r
- // slider.setPaintTicks(true);\r
- slider.setBackground(Color.white);\r
- slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
- slider.setOrientation(0);\r
- valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
- valueField.setText(" ");\r
- valueField.addActionListener(this);\r
- label.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label.setText("set this label text");\r
- jPanel1.setLayout(borderLayout1);\r
- jPanel2.setLayout(flowLayout1);\r
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- applyButton.setLabel("Apply");\r
- applyButton.addActionListener(this);\r
- undoButton.setEnabled(false);\r
- undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- undoButton.setLabel("Undo");\r
- undoButton.addActionListener(this);\r
- allGroupsCheck.setEnabled(false);\r
- allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
- allGroupsCheck.setLabel("Apply threshold to all groups");\r
- allGroupsCheck.setName("Apply to all Groups");\r
- this.setBackground(Color.white);\r
- this.setForeground(Color.black);\r
- jPanel2.add(label, null);\r
- jPanel2.add(applyButton, null);\r
- jPanel2.add(undoButton, null);\r
- jPanel2.add(allGroupsCheck);\r
- jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
- jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
- protected void applyButton_actionPerformed()\r
- { }\r
-\r
- protected void undoButton_actionPerformed()\r
- { }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- { }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
- public void mouseExited(MouseEvent evt)\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.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class SliderPanel extends Panel implements ActionListener,
+ AdjustmentListener, MouseListener
+{
+ AlignmentPanel ap;
+
+ boolean forConservation = true;
+
+ ColourSchemeI cs;
+
+ static Frame conservationSlider;
+
+ static Frame PIDSlider;
+
+ public static int setConservationSlider(AlignmentPanel ap,
+ ColourSchemeI cs, String source)
+ {
+ SliderPanel sp = null;
+
+ if (conservationSlider == null)
+ {
+ sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+ conservationSlider = new Frame();
+ conservationSlider.add(sp);
+ }
+ else
+ {
+ sp = (SliderPanel) conservationSlider.getComponent(0);
+ sp.cs = cs;
+ }
+
+ conservationSlider.setTitle("Conservation Colour Increment (" + source
+ + ")");
+ if (ap.av.alignment.getGroups() != null)
+ {
+ sp.setAllGroupsCheckEnabled(true);
+ }
+ else
+ {
+ sp.setAllGroupsCheckEnabled(false);
+ }
+
+ return sp.getValue();
+ }
+
+ public static void showConservationSlider()
+ {
+ try
+ {
+ PIDSlider.setVisible(false);
+ PIDSlider = null;
+ } catch (Exception ex)
+ {
+ }
+
+ if (!conservationSlider.isVisible())
+ {
+ jalview.bin.JalviewLite.addFrame(conservationSlider,
+ conservationSlider.getTitle(), 420, 100);
+ conservationSlider.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ conservationSlider = null;
+ }
+ });
+
+ }
+
+ }
+
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+ String source)
+ {
+ SliderPanel pid = null;
+ if (PIDSlider == null)
+ {
+ pid = new SliderPanel(ap, 50, false, cs);
+ PIDSlider = new Frame();
+ PIDSlider.add(pid);
+ }
+ else
+ {
+ pid = (SliderPanel) PIDSlider.getComponent(0);
+ pid.cs = cs;
+ }
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+ if (ap.av.alignment.getGroups() != null)
+ {
+ pid.setAllGroupsCheckEnabled(true);
+ }
+ else
+ {
+ pid.setAllGroupsCheckEnabled(false);
+ }
+
+ return pid.getValue();
+
+ }
+
+ public static void showPIDSlider()
+ {
+ try
+ {
+ conservationSlider.setVisible(false);
+ conservationSlider = null;
+ } catch (Exception ex)
+ {
+ }
+
+ if (!PIDSlider.isVisible())
+ {
+ jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
+ 420, 100);
+ PIDSlider.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ PIDSlider = null;
+ }
+ });
+ }
+
+ }
+
+ public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
+ ColourSchemeI cs)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ this.ap = ap;
+ this.cs = cs;
+ forConservation = forConserve;
+ undoButton.setVisible(false);
+ applyButton.setVisible(false);
+ if (forConservation)
+ {
+ label.setText("Modify conservation visibility");
+ slider.setMinimum(0);
+ slider.setMaximum(50 + slider.getVisibleAmount());
+ slider.setUnitIncrement(1);
+ }
+ else
+ {
+ label.setText("Colour residues above % occurence");
+ slider.setMinimum(0);
+ slider.setMaximum(100 + slider.getVisibleAmount());
+ slider.setBlockIncrement(1);
+ }
+
+ slider.addAdjustmentListener(this);
+ slider.addMouseListener(this);
+
+ slider.setValue(value);
+ valueField.setText(value + "");
+ }
+
+ public void valueChanged(int i)
+ {
+ if (cs == null)
+ {
+ return;
+ }
+
+ ColourSchemeI toChange = null;
+ Vector allGroups = null;
+ int groupIndex = 0;
+
+ if (allGroupsCheck.getState())
+ {
+ allGroups = ap.av.alignment.getGroups();
+ groupIndex = allGroups.size() - 1;
+ }
+ else
+ {
+ toChange = cs;
+ }
+
+ while (groupIndex > -1)
+ {
+ if (allGroups != null)
+ {
+ toChange = ((SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+ }
+
+ if (forConservation)
+ {
+ toChange.setConservationInc(i);
+ }
+ else
+ {
+ toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+ }
+
+ groupIndex--;
+ }
+
+ ap.seqPanel.seqCanvas.repaint();
+
+ }
+
+ public void setAllGroupsCheckEnabled(boolean b)
+ {
+ allGroupsCheck.setEnabled(b);
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == applyButton)
+ {
+ applyButton_actionPerformed();
+ }
+ else if (evt.getSource() == undoButton)
+ {
+ undoButton_actionPerformed();
+ }
+ else if (evt.getSource() == valueField)
+ {
+ valueField_actionPerformed();
+ }
+ }
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ valueChanged(slider.getValue());
+ }
+
+ public void valueField_actionPerformed()
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ } catch (Exception ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
+ public void setValue(int value)
+ {
+ slider.setValue(value);
+ }
+
+ public int getValue()
+ {
+ return Integer.parseInt(valueField.getText());
+ }
+
+ // this is used for conservation colours, PID colours and redundancy threshold
+ protected Scrollbar slider = new Scrollbar();
+
+ protected TextField valueField = new TextField();
+
+ protected Label label = new Label();
+
+ Panel jPanel1 = new Panel();
+
+ Panel jPanel2 = new Panel();
+
+ protected Button applyButton = new Button();
+
+ protected Button undoButton = new Button();
+
+ FlowLayout flowLayout1 = new FlowLayout();
+
+ protected Checkbox allGroupsCheck = new Checkbox();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ FlowLayout flowLayout2 = new FlowLayout();
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout2);
+
+ // slider.setMajorTickSpacing(10);
+ // slider.setMinorTickSpacing(1);
+ // slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setFont(new java.awt.Font("Verdana", 0, 11));
+ slider.setOrientation(0);
+ valueField.setFont(new java.awt.Font("Verdana", 0, 11));
+ valueField.setText(" ");
+ valueField.addActionListener(this);
+ label.setFont(new java.awt.Font("Verdana", 0, 11));
+ label.setText("set this label text");
+ jPanel1.setLayout(borderLayout1);
+ jPanel2.setLayout(flowLayout1);
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+ applyButton.setLabel("Apply");
+ applyButton.addActionListener(this);
+ undoButton.setEnabled(false);
+ undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
+ undoButton.setLabel("Undo");
+ undoButton.addActionListener(this);
+ allGroupsCheck.setEnabled(false);
+ allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
+ allGroupsCheck.setLabel("Apply threshold to all groups");
+ allGroupsCheck.setName("Apply to all Groups");
+ this.setBackground(Color.white);
+ this.setForeground(Color.black);
+ jPanel2.add(label, null);
+ jPanel2.add(applyButton, null);
+ jPanel2.add(undoButton, null);
+ jPanel2.add(allGroupsCheck);
+ jPanel1.add(valueField, java.awt.BorderLayout.EAST);
+ jPanel1.add(slider, java.awt.BorderLayout.CENTER);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ }
+
+ protected void applyButton_actionPerformed()
+ {
+ }
+
+ protected void undoButton_actionPerformed()
+ {
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true);
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff