+/*\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 jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
import java.awt.event.*;\r
-import javax.swing.event.*;\r
import javax.swing.*;\r
-import java.util.*;\r
+import javax.swing.event.*;\r
\r
-public class SliderPanel extends GSliderPanel\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SliderPanel\r
+ extends GSliderPanel\r
{\r
+ static JInternalFrame conservationSlider;\r
+ static JInternalFrame PIDSlider;\r
AlignmentPanel ap;\r
boolean forConservation = true;\r
ColourSchemeI cs;\r
\r
- static JInternalFrame conservationSlider;\r
- static JInternalFrame PIDSlider;\r
+ /**\r
+ * Creates a new SliderPanel object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param value DOCUMENT ME!\r
+ * @param forConserve DOCUMENT ME!\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
+ ColourSchemeI cs)\r
+ {\r
+ this.ap = ap;\r
+ this.cs = cs;\r
+ forConservation = forConserve;\r
+ undoButton.setVisible(false);\r
+ applyButton.setVisible(false);\r
\r
- public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs, String source)\r
+ if (forConservation)\r
+ {\r
+ label.setText("Enter value to increase conservation visibility");\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100);\r
+ }\r
+ else\r
+ {\r
+ label.setText("Enter % identity above which to colour residues");\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100);\r
+ }\r
+\r
+ slider.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ valueChanged(slider.getValue());\r
+ }\r
+ });\r
+\r
+ slider.setValue(value);\r
+ valueField.setText(value + "");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param cs DOCUMENT ME!\r
+ * @param source DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static int setConservationSlider(AlignmentPanel ap,\r
+ ColourSchemeI cs, String source)\r
{\r
SliderPanel sp = null;\r
- ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
- int value = ccs.inc;\r
\r
- if(conservationSlider == null)\r
+ if (conservationSlider == null)\r
{\r
- sp = new SliderPanel(ap, value, true, cs);\r
+ sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);\r
conservationSlider = new JInternalFrame();\r
conservationSlider.setContentPane(sp);\r
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
else\r
{\r
- sp = (SliderPanel)conservationSlider.getContentPane();\r
- sp.cs = cs;\r
- sp.setValue(value);\r
+ sp = (SliderPanel) conservationSlider.getContentPane();\r
+ sp.cs = cs;\r
}\r
\r
- conservationSlider.setTitle("Conservation Colour Increment ("+source+")");\r
- if(ap.av.alignment.getGroups()!=null)\r
- sp.setAllGroupsCheckEnabled( true );\r
+ conservationSlider.setTitle("Conservation Colour Increment (" +\r
+ source + ")");\r
+\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ sp.setAllGroupsCheckEnabled(true);\r
+ }\r
else\r
- sp.setAllGroupsCheckEnabled( false);\r
+ {\r
+ sp.setAllGroupsCheckEnabled(false);\r
+ }\r
\r
return sp.getValue();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public static void showConservationSlider()\r
{\r
- try{\r
+ try\r
+ {\r
PIDSlider.setClosed(true);\r
PIDSlider = null;\r
- }catch(Exception ex){}\r
-\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- if(!conservationSlider.isVisible())\r
+ if (!conservationSlider.isVisible())\r
{\r
- Desktop.addInternalFrame(conservationSlider, conservationSlider.getTitle(), 420, 90, false);\r
+ Desktop.addInternalFrame(conservationSlider,\r
+ conservationSlider.getTitle(), 420, 90, false);\r
conservationSlider.addInternalFrameListener(new javax.swing.event.\r
InternalFrameAdapter()\r
{\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
{\r
conservationSlider = null;\r
}\r
});\r
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
-\r
}\r
\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel pid = null;\r
- if(PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, 50, false, cs);\r
- PIDSlider = new JInternalFrame();\r
- PIDSlider.setContentPane(pid);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel)PIDSlider.getContentPane();\r
- pid.cs = cs;\r
- }\r
- PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- pid.setAllGroupsCheckEnabled(true);\r
- else\r
- pid.setAllGroupsCheckEnabled(false);\r
-\r
- return pid.getValue();\r
-\r
- }\r
-\r
- public static void showPIDSlider()\r
- {\r
- try{\r
- conservationSlider.setClosed(true);\r
- conservationSlider = null;\r
- }catch(Exception ex){}\r
-\r
- if(!PIDSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90, false);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- PIDSlider.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
- {\r
- PIDSlider = null;\r
- }\r
- });\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param cs DOCUMENT ME!\r
+ * @param source DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
+ {\r
+ SliderPanel pid = null;\r
+\r
+ int threshold = cs.getThreshold();\r
+\r
+ if (PIDSlider == null)\r
+ {\r
+ pid = new SliderPanel(ap, threshold, false, cs);\r
+ PIDSlider = new JInternalFrame();\r
+ PIDSlider.setContentPane(pid);\r
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
+ else\r
+ {\r
+ pid = (SliderPanel) PIDSlider.getContentPane();\r
+ pid.cs = cs;\r
+ }\r
\r
- }\r
-\r
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, ColourSchemeI cs)\r
- {\r
- this.ap = ap;\r
- this.cs = cs;\r
- forConservation = forConserve;\r
- undoButton.setVisible(false);\r
- applyButton.setVisible(false);\r
- if(forConservation)\r
+ if (ap.av.alignment.getGroups() != null)\r
{\r
- label.setText("Enter the value by which to decrease conservation colour intensity");\r
- slider.setMinimum(0);\r
- slider.setMaximum(50);\r
+ pid.setAllGroupsCheckEnabled(true);\r
}\r
else\r
{\r
- label.setText("Enter the percent identity above which to colour residues");\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
+ pid.setAllGroupsCheckEnabled(false);\r
}\r
\r
+ return pid.getValue();\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public static void showPIDSlider()\r
+ {\r
+ try\r
+ {\r
+ conservationSlider.setClosed(true);\r
+ conservationSlider = null;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- slider.addChangeListener( new ChangeListener()\r
+ if (!PIDSlider.isVisible())\r
{\r
- public void stateChanged(ChangeEvent evt)\r
+ Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,\r
+ false);\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ PIDSlider.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
{\r
- valueField.setText( slider.getValue()+"" );\r
- valueChanged( slider.getValue() );\r
- }\r
- });\r
-\r
- slider.setValue(value);\r
- valueField.setText(value+"");\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
+ {\r
+ PIDSlider = null;\r
+ }\r
+ });\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
public void valueChanged(int i)\r
{\r
- if(cs == null)\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.isSelected())\r
+ if (allGroupsCheck.isSelected())\r
{\r
allGroups = ap.av.alignment.getGroups();\r
- groupIndex = allGroups.size()-1;\r
+ groupIndex = allGroups.size() - 1;\r
}\r
else\r
+ {\r
toChange = cs;\r
+ }\r
\r
-\r
- while( groupIndex > -1 )\r
+ while (groupIndex > -1)\r
{\r
- if(allGroups!=null)\r
- toChange = ((SequenceGroup)allGroups.get(groupIndex)).cs;\r
+ if (allGroups != null)\r
+ {\r
+ toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;\r
+\r
+ if (toChange == null)\r
+ {\r
+ groupIndex--;\r
+\r
+ continue;\r
+ }\r
+ }\r
\r
if (forConservation)\r
{\r
- if (toChange instanceof ConservationColourScheme)\r
- ( (ConservationColourScheme) toChange).inc = i;\r
+ if (toChange.conservationApplied())\r
+ {\r
+ toChange.setConservationInc(i);\r
+ }\r
}\r
else\r
{\r
- if (toChange.canThreshold())\r
- ( (ResidueColourScheme) toChange).setThreshold(i);\r
+ toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
groupIndex--;\r
}\r
\r
- ap.seqPanel.repaint();\r
-\r
+ ap.seqPanel.seqCanvas.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
public void setAllGroupsCheckEnabled(boolean b)\r
{\r
allGroupsCheck.setEnabled(b);\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (NumberFormatException ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param value DOCUMENT ME!\r
+ */\r
public void setValue(int value)\r
{\r
slider.setValue(value);\r
}\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getValue()\r
{\r
return Integer.parseInt(valueField.getText());\r
}\r
\r
+ public void slider_mouseReleased(MouseEvent e)\r
+ {\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff