-<?xml version="1.0" encoding="UTF-8"?>\r
-<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->\r
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
- <xs:complexType name="VAMSAS">\r
- <xs:sequence>\r
- <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>\r
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>\r
- </xs:sequence>\r
- </xs:complexType>\r
- <xs:element name="SequenceSet">\r
- <xs:complexType>\r
- <xs:sequence>\r
- <xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">\r
- <xs:complexType>\r
- <xs:complexContent>\r
- <xs:extension base="vamsas:SequenceType">\r
- <xs:sequence>\r
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">\r
- <xs:complexType>\r
- <xs:attribute name="source" type="xs:string"/>\r
- <xs:attribute name="version" type="xs:string"/>\r
- <xs:attribute name="accessionId" type="xs:string"/>\r
- </xs:complexType>\r
- </xs:element>\r
- </xs:sequence>\r
- </xs:extension>\r
- </xs:complexContent>\r
- </xs:complexType>\r
- </xs:element>\r
- <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">\r
- <xs:complexType>\r
- <xs:sequence>\r
- <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>\r
- <xs:element name="label" type="xs:string"/>\r
- <xs:element name="description" type="xs:string" minOccurs="0"/>\r
- <xs:element name="thresholdLine" minOccurs="0">\r
- <xs:complexType>\r
- <xs:attribute name="label" type="xs:string"/>\r
- <xs:attribute name="value" type="xs:float"/>\r
- <xs:attribute name="colour" type="xs:int"/>\r
- </xs:complexType>\r
- </xs:element>\r
- </xs:sequence>\r
- <xs:attribute name="graph" type="xs:boolean" use="required"/>\r
- <xs:attribute name="graphType" type="xs:int" use="optional"/>\r
- <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>\r
- <xs:attribute name="graphColour" type="xs:int" use="optional"/>\r
- <xs:attribute name="graphGroup" type="xs:int" use="optional"/>\r
- <xs:attribute name="id" type="xs:string" use="optional"/>\r
- </xs:complexType>\r
- </xs:element>\r
- </xs:sequence>\r
- <xs:attribute name="gapChar" type="xs:string" use="required"/>\r
- </xs:complexType>\r
- </xs:element>\r
- <xs:element name="annotationElement">\r
- <xs:complexType>\r
- <xs:sequence>\r
- <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>\r
- <xs:element name="description" type="xs:string" minOccurs="0"/>\r
- <xs:element name="secondaryStructure" minOccurs="0">\r
- <xs:simpleType>\r
- <xs:restriction base="xs:string">\r
- <xs:length value="1"/>\r
- </xs:restriction>\r
- </xs:simpleType>\r
- </xs:element>\r
- <xs:element name="value" type="xs:float" minOccurs="0"/>\r
- </xs:sequence>\r
- <xs:attribute name="position" type="xs:int" use="required"/>\r
- <xs:attribute name="colour" type="xs:int" use="optional"/>\r
- </xs:complexType>\r
- </xs:element>\r
- <xs:complexType name="SequenceType">\r
- <xs:sequence>\r
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>\r
- <xs:element name="name" type="xs:string" minOccurs="0"/>\r
- </xs:sequence>\r
- <xs:attribute name="id" type="xs:string"/>\r
- <xs:attribute name="description" type="xs:string"/>\r
- </xs:complexType>\r
-</xs:schema>\r
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:complexType name="VAMSAS">
+ <xs:sequence>
+ <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:element name="SequenceSet">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:SequenceType">
+ <xs:sequence>
+ <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="source" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="accessionId" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="label" type="xs:string"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="thresholdLine" minOccurs="0">
+ <xs:complexType>
+ <xs:attribute name="label" type="xs:string"/>
+ <xs:attribute name="value" type="xs:float"/>
+ <xs:attribute name="colour" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="graph" type="xs:boolean" use="required"/>
+ <xs:attribute name="graphType" type="xs:int" use="optional"/>
+ <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
+ <xs:attribute name="graphColour" type="xs:int" use="optional"/>
+ <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
+ <xs:attribute name="id" type="xs:string" use="optional"/>
+ <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
+ <xs:attribute name="score" type="xs:float" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="gapChar" type="xs:string" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="annotationElement">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="secondaryStructure" minOccurs="0">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:length value="1"/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ <xs:element name="value" type="xs:float" minOccurs="0"/>
+ </xs:sequence>
+ <xs:attribute name="position" type="xs:int" use="required"/>
+ <xs:attribute name="colour" type="xs:int" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:complexType name="SequenceType">
+ <xs:sequence>
+ <xs:element name="sequence" type="xs:string" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:string"/>
+ <xs:attribute name="description" type="xs:string"/>
+ </xs:complexType>
+</xs:schema>
if (annotations[i].autoCalculated) {\r
continue;\r
}\r
-\r
- aSize = aslen; // aa alignment width.\r
- jalview.datamodel.Annotation[] anots =\r
- new jalview.datamodel.Annotation[aSize];\r
\r
- for (a = 0; a < aSize; a++)\r
+ aSize = aslen; // aa alignment width.\r
+ jalview.datamodel.Annotation[] anots = \r
+ (annotations[i].annotations==null) \r
+ ? null :\r
+ new jalview.datamodel.Annotation[aSize];\r
+ if (anots!=null)\r
{\r
- // process through codon map.\r
- if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))\r
+ for (a = 0; a < aSize; a++)\r
{\r
- pos = codons[a][0];\r
- if (annotations[i].annotations[pos] == null\r
- || annotations[i].annotations[pos] == null)\r
- continue;\r
+ // process through codon map.\r
+ if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))\r
+ {\r
+ pos = codons[a][0];\r
+ if (annotations[i].annotations[pos] == null\r
+ || annotations[i].annotations[pos] == null)\r
+ continue;\r
\r
- anots[a] = new Annotation(annotations[i].annotations[pos]);\r
+ anots[a] = new Annotation(annotations[i].annotations[pos]);\r
+ }\r
}\r
}\r
\r
jalview.datamodel.AlignmentAnnotation aa\r
= new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
annotations[i].description, anots);\r
+ if (annotations[i].hasScore)\r
+ {\r
+ aa.setScore(annotations[i].getScore());\r
+ }\r
al.addAnnotation(aa);\r
}\r
}\r
-/*\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
-\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
-\r
-public class AnnotationLabels\r
- extends Panel implements ActionListener, MouseListener, MouseMotionListener\r
-{\r
- Image image;\r
- boolean active = false;\r
- AlignmentPanel ap;\r
- AlignViewport av;\r
- boolean resizing = false;\r
- int oldY, mouseX;\r
-\r
- static String ADDNEW = "Add New Row";\r
- static String EDITNAME = "Edit Label/Description";\r
- static String HIDE = "Hide This Row";\r
- static String SHOWALL = "Show All Hidden Rows";\r
- static String OUTPUT_TEXT = "Show Values In Textbox";\r
- static String COPYCONS_SEQ = "Copy Consensus Sequence";\r
-\r
- int scrollOffset = 0;\r
- int selectedRow = -1;\r
-\r
- Tooltip tooltip;\r
-\r
- public AnnotationLabels(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- this.av = ap.av;\r
- setLayout(null);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
-\r
- public AnnotationLabels(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void setScrollOffset(int y)\r
- {\r
- scrollOffset = y;\r
- repaint();\r
- }\r
-\r
- int getSelectedRow(int y)\r
- {\r
- int row = -1;\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- if (aa == null)\r
- {\r
- return row;\r
- }\r
-\r
- int height = 0;\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- continue;\r
- }\r
-\r
- height += aa[i].height;\r
- if (y < height)\r
- {\r
- row = i;\r
- break;\r
- }\r
- }\r
-\r
- return row;\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- if (evt.getActionCommand().equals(ADDNEW))\r
- {\r
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",\r
- null,\r
- new Annotation[ap.av.alignment.getWidth()]);\r
-\r
- if (!editLabelDescription(newAnnotation))\r
- {\r
- return;\r
- }\r
-\r
- ap.av.alignment.addAnnotation(newAnnotation);\r
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);\r
- }\r
- else if (evt.getActionCommand().equals(EDITNAME))\r
- {\r
- editLabelDescription(aa[selectedRow]);\r
- }\r
- else if (evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
- }\r
- else if (evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- aa[i].visible = true;\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- ap.alignFrame.getTitle() + " - " +\r
- aa[selectedRow].label, 500, 100);\r
- cap.setText(aa[selectedRow].toString());\r
- }\r
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))\r
- {\r
- SequenceI cons = av.getConsensusSeq();\r
- if (cons != null)\r
- {\r
- copy_annotseqtoclipboard(cons);\r
- }\r
-\r
- }\r
- ap.annotationPanel.adjustPanelHeight();\r
- setSize(getSize().width, ap.annotationPanel.getSize().height);\r
- ap.validate();\r
- ap.paintAlignment(true);\r
- }\r
-\r
- boolean editLabelDescription(AlignmentAnnotation annotation)\r
- {\r
- EditNameDialog dialog = new EditNameDialog(\r
- annotation.label,\r
- annotation.description,\r
- " Annotation Label",\r
- "Annotation Description",\r
- ap.alignFrame,\r
- "Edit Annotation Name / Description",\r
- 500, 100);\r
-\r
- if (dialog.accept)\r
- {\r
- annotation.label = dialog.getName();\r
- annotation.description = dialog.getDescription();\r
- repaint();\r
- return true;\r
- }\r
- else\r
- return false;\r
-\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- int row = getSelectedRow(evt.getY() - scrollOffset);\r
-\r
- if (row > -1)\r
- {\r
- if (tooltip == null)\r
- {\r
- tooltip = new Tooltip(ap.av.alignment.\r
- getAlignmentAnnotation()[row].\r
- description,\r
- this);\r
- }\r
- else\r
- {\r
- tooltip.setTip(ap.av.alignment.\r
- getAlignmentAnnotation()[row].description);\r
- }\r
- }\r
- else if (tooltip != null)\r
- {\r
- tooltip.setTip("");\r
- }\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {}\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {}\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = getSelectedRow(evt.getY() - scrollOffset);\r
-\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- PopupMenu popup = new PopupMenu("Annotations");\r
-\r
- MenuItem item = new MenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- popup.add(item);\r
- item = new MenuItem(EDITNAME);\r
- item.addActionListener(this);\r
- popup.add(item);\r
- item = new MenuItem(HIDE);\r
- item.addActionListener(this);\r
- popup.add(item);\r
- item = new MenuItem(SHOWALL);\r
- item.addActionListener(this);\r
- popup.add(item);\r
- this.add(popup);\r
- item = new MenuItem(OUTPUT_TEXT);\r
- item.addActionListener(this);\r
- popup.add(item);\r
-\r
- if (aa[selectedRow] == ap.av.consensus)\r
- {\r
- popup.addSeparator();\r
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(\r
- "Ignore Gaps In Consensus",\r
- ap.av.getIgnoreGapsConsensus());\r
-\r
- cbmi.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- ap.av.setIgnoreGapsConsensus(cbmi.getState());\r
- ap.paintAlignment(true);\r
- }\r
- });\r
- popup.add(cbmi);\r
- item = new MenuItem(COPYCONS_SEQ);\r
- item.addActionListener(this);\r
- popup.add(item);\r
- }\r
-\r
- popup.show(this, evt.getX(), evt.getY());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void copy_annotseqtoclipboard(SequenceI sq)\r
- {\r
- if (sq == null || sq.getLength() < 1)\r
- {\r
- return;\r
- }\r
- jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();\r
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +\r
- sq.getStart() + "\t" +\r
- sq.getEnd() + "\t" +\r
- sq.getSequenceAsString() + "\n");\r
- if (av.hasHiddenColumns)\r
- {\r
- jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();\r
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)\r
- {\r
- int[] region = (int[])\r
- av.getColumnSelection().getHiddenColumns().elementAt(i);\r
-\r
- jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]\r
- {region[0],\r
- region[1]});\r
- }\r
- }\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- int w = getSize().width;\r
- if (image == null || w != image.getWidth(this))\r
- {\r
- image = createImage(w, ap.annotationPanel.getSize().height);\r
- }\r
-\r
- drawComponent(image.getGraphics(), w);\r
- g.drawImage(image, 0, 0, this);\r
- }\r
-\r
- public void drawComponent(Graphics g, int width)\r
- {\r
- g.setFont(av.getFont());\r
- FontMetrics fm = g.getFontMetrics(av.getFont());\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
-\r
- g.translate(0, scrollOffset);\r
- g.setColor(Color.black);\r
-\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\r
- if (aa != null)\r
- {\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- continue;\r
- }\r
-\r
- x = width - fm.stringWidth(aa[i].label) - 3;\r
-\r
- if (aa[i].graph > 0)\r
- {\r
- y += (aa[i].height / 3);\r
- }\r
-\r
- g.drawString(aa[i].label, x, y);\r
-\r
- if (aa[i].graph > 0)\r
- {\r
- y += (2 * aa[i].height / 3);\r
- }\r
- else\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationLabels
+ extends Panel implements ActionListener, MouseListener, MouseMotionListener
+{
+ Image image;
+ boolean active = false;
+ AlignmentPanel ap;
+ AlignViewport av;
+ boolean resizing = false;
+ int oldY, mouseX;
+
+ static String ADDNEW = "Add New Row";
+ static String EDITNAME = "Edit Label/Description";
+ static String HIDE = "Hide This Row";
+ static String SHOWALL = "Show All Hidden Rows";
+ static String OUTPUT_TEXT = "Show Values In Textbox";
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
+ int scrollOffset = 0;
+ int selectedRow = -1;
+
+ Tooltip tooltip;
+
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ setLayout(null);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ }
+
+ public AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public void setScrollOffset(int y)
+ {
+ scrollOffset = y;
+ repaint();
+ }
+
+ int getSelectedRow(int y)
+ {
+ int row = -1;
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if (aa == null)
+ {
+ return row;
+ }
+
+ int height = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+
+ height += aa[i].height;
+ if (y < height)
+ {
+ row = i;
+ break;
+ }
+ }
+
+ return row;
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",
+ null,
+ new Annotation[ap.av.alignment.getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.alignment.addAnnotation(newAnnotation);
+ ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ aa[i].visible = (aa[i].annotations==null) ? false : true;
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ ap.alignFrame.getTitle() + " - " +
+ aa[selectedRow].label, 500, 100);
+ cap.setText(aa[selectedRow].toString());
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
+
+ }
+ ap.annotationPanel.adjustPanelHeight();
+ setSize(getSize().width, ap.annotationPanel.getSize().height);
+ ap.validate();
+ ap.paintAlignment(true);
+ }
+
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ EditNameDialog dialog = new EditNameDialog(
+ annotation.label,
+ annotation.description,
+ " Annotation Label",
+ "Annotation Description",
+ ap.alignFrame,
+ "Edit Annotation Name / Description",
+ 500, 100);
+
+ if (dialog.accept)
+ {
+ annotation.label = dialog.getName();
+ annotation.description = dialog.getDescription();
+ repaint();
+ return true;
+ }
+ else
+ return false;
+
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ int row = getSelectedRow(evt.getY() - scrollOffset);
+
+ if (row > -1)
+ {
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(ap.av.alignment.
+ getAlignmentAnnotation()[row].
+ description,
+ this);
+ }
+ else
+ {
+ tooltip.setTip(ap.av.alignment.
+ getAlignmentAnnotation()[row].description);
+ }
+ }
+ else if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {}
+
+ public void mouseClicked(MouseEvent evt)
+ {}
+
+ public void mouseReleased(MouseEvent evt)
+ {}
+
+ public void mouseEntered(MouseEvent evt)
+ {}
+
+ public void mouseExited(MouseEvent evt)
+ {}
+
+ public void mousePressed(MouseEvent evt)
+ {
+ selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ PopupMenu popup = new PopupMenu("Annotations");
+
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(EDITNAME);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(HIDE);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ this.add(popup);
+ item = new MenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ popup.add(item);
+
+ if (aa[selectedRow] == ap.av.consensus)
+ {
+ popup.addSeparator();
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+ "Ignore Gaps In Consensus",
+ ap.av.getIgnoreGapsConsensus());
+
+ cbmi.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ ap.paintAlignment(true);
+ }
+ });
+ popup.add(cbmi);
+ item = new MenuItem(COPYCONS_SEQ);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+
+ popup.show(this, evt.getX(), evt.getY());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void copy_annotseqtoclipboard(SequenceI sq)
+ {
+ if (sq == null || sq.getLength() < 1)
+ {
+ return;
+ }
+ jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+ jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
+ sq.getStart() + "\t" +
+ sq.getEnd() + "\t" +
+ sq.getSequenceAsString() + "\n");
+ if (av.hasHiddenColumns)
+ {
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[])
+ av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+ jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
+ {region[0],
+ region[1]});
+ }
+ }
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+ int w = getSize().width;
+ if (image == null || w != image.getWidth(this))
+ {
+ image = createImage(w, ap.annotationPanel.getSize().height);
+ }
+
+ drawComponent(image.getGraphics(), w);
+ g.drawImage(image, 0, 0, this);
+ }
+
+ public void drawComponent(Graphics g, int width)
+ {
+ g.setFont(av.getFont());
+ FontMetrics fm = g.getFontMetrics(av.getFont());
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+
+ g.translate(0, scrollOffset);
+ g.setColor(Color.black);
+
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ int y = g.getFont().getSize();
+ int x = 0;
+
+ if (aa != null)
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+
+ x = width - fm.stringWidth(aa[i].label) - 3;
+
+ if (aa[i].graph > 0)
+ {
+ y += (aa[i].height / 3);
+ }
+
+ g.drawString(aa[i].label, x, y);
+
+ if (aa[i].graph > 0)
+ {
+ y += (2 * aa[i].height / 3);
+ }
+ else
+ {
+ y += aa[i].height;
+ }
+ }
+ }
+ }
+
+}
}
int tSize = 0;
-
+ if (annotations[a].annotations == null)
+ {
+ // nothing to edit here ?
+ continue;
+ }
aSize = annotations[a].annotations.length;
if (insert)
{
/** DOCUMENT ME!! */
public float graphMax;
+ /**
+ * Score associated with label and description.
+ */
public float score;
-
+ /**
+ * flag indicating if annotation has a score.
+ */
+ public boolean hasScore=false;
+
public GraphLine threshold;
// Graphical hints and tips
* if appropriate.
*/
private void validateRangeAndDisplay() {
+ if (annotations==null)
+ {
+ visible=false; // try to prevent renderer from displaying.
+ return; // this is a non-annotation row annotation - ie a sequence score.
+ }
int graphType = graph;
float min = graphMin;
float max = graphMax;
{
return;
}
-
+ if (annotations==null)
+ {
+ return;
+ }
sequenceMapping = new java.util.Hashtable();
sequenceRef = seqRef;
if (sequenceRef==null)
return;
+ if (annotations==null)
+ {
+ return;
+ }
+
int a = 0, aSize = sequenceRef.getLength();
if (aSize == 0)
sequenceRef = null;
}
}
+
+ /**
+ * @return the score
+ */
+ public float getScore()
+ {
+ return score;
+ }
+
+ /**
+ * @param score the score to set
+ */
+ public void setScore(float score)
+ {
+ this.score = score;
+ }
+ /**
+ *
+ * @return true if annotation has an associated score
+ */
+ public boolean hasScore()
+ {
+ return hasScore;
+ }
}
{
for (int i = 0; i < aa.length; i++)
{
- if (!aa[i].visible)
+ if (!aa[i].visible && aa[i].annotations!=null)
{
dif += aa[i].height;
aa[i].visible = true;
}
an.setLabel(aa[i].label);
-
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
AnnotationElement ae;
-
- for (int a = 0; a < aa[i].annotations.length; a++)
+ if (aa[i].annotations!=null)
{
- if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
{
- continue;
- }
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
- ae.setValue(aa[i].annotations[a].value);
- ae.setPosition(a);
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
- "");
+ ae = new AnnotationElement();
+ ae.setDescription(aa[i].annotations[a].description);
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ ae.setValue(aa[i].annotations[a].value);
+ ae.setPosition(a);
+ ae
+ .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
- if (aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
+ if (aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
- an.addAnnotationElement(ae);
+ an.addAnnotationElement(ae);
+ }
+ } else {
+ an.setScoreOnly(true);
}
-
vamsasSet.addAnnotation(an);
}
}
}
AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
- al.getWidth()];
+ jalview.datamodel.Annotation[] anot = null;
+ if (!an[i].getScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[
+ al.getWidth()];
- for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
- {
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
- getDisplayCharacter(),
- ae[aa].getDescription(),
- ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
- ae[aa].getSecondaryStructure().charAt(0),
- ae[aa].getValue());
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
- getColour());
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ {
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
+ getDisplayCharacter(),
+ ae[aa].getDescription(),
+ ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
+ ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue());
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
+ getColour());
+ }
}
-
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
);
al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
-
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
+ }
al.addAnnotation(jaa);
}
}
{\r
row = annotations[i];\r
\r
- if (!row.visible)\r
+ if (!row.visible && row.annotations!=null)\r
{\r
continue;\r
}\r
private java.lang.String _id;\r
\r
/**\r
+ * Field _scoreOnly\r
+ */\r
+ private boolean _scoreOnly = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _scoreOnly\r
+ */\r
+ private boolean _has_scoreOnly;\r
+\r
+ /**\r
+ * Field _score\r
+ */\r
+ private float _score;\r
+\r
+ /**\r
+ * keeps track of state for field: _score\r
+ */\r
+ private boolean _has_score;\r
+\r
+ /**\r
* Field _annotationElementList\r
*/\r
private java.util.Vector _annotationElementList;\r
} //-- void deleteGraphType() \r
\r
/**\r
+ * Method deleteScore\r
+ * \r
+ */\r
+ public void deleteScore()\r
+ {\r
+ this._has_score= false;\r
+ } //-- void deleteScore() \r
+\r
+ /**\r
+ * Method deleteScoreOnly\r
+ * \r
+ */\r
+ public void deleteScoreOnly()\r
+ {\r
+ this._has_scoreOnly= false;\r
+ } //-- void deleteScoreOnly() \r
+\r
+ /**\r
* Method enumerateAnnotationElement\r
* \r
* \r
} //-- java.lang.String getLabel() \r
\r
/**\r
+ * Returns the value of field 'score'.\r
+ * \r
+ * @return float\r
+ * @return the value of field 'score'.\r
+ */\r
+ public float getScore()\r
+ {\r
+ return this._score;\r
+ } //-- float getScore() \r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'scoreOnly'.\r
+ */\r
+ public boolean getScoreOnly()\r
+ {\r
+ return this._scoreOnly;\r
+ } //-- boolean getScoreOnly() \r
+\r
+ /**\r
* Returns the value of field 'sequenceRef'.\r
* \r
* @return String\r
} //-- boolean hasGraphType() \r
\r
/**\r
+ * Method hasScore\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasScore()\r
+ {\r
+ return this._has_score;\r
+ } //-- boolean hasScore() \r
+\r
+ /**\r
+ * Method hasScoreOnly\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasScoreOnly()\r
+ {\r
+ return this._has_scoreOnly;\r
+ } //-- boolean hasScoreOnly() \r
+\r
+ /**\r
* Method isValid\r
* \r
* \r
} //-- void setLabel(java.lang.String) \r
\r
/**\r
+ * Sets the value of field 'score'.\r
+ * \r
+ * @param score the value of field 'score'.\r
+ */\r
+ public void setScore(float score)\r
+ {\r
+ this._score = score;\r
+ this._has_score = true;\r
+ } //-- void setScore(float) \r
+\r
+ /**\r
+ * Sets the value of field 'scoreOnly'.\r
+ * \r
+ * @param scoreOnly the value of field 'scoreOnly'.\r
+ */\r
+ public void setScoreOnly(boolean scoreOnly)\r
+ {\r
+ this._scoreOnly = scoreOnly;\r
+ this._has_scoreOnly = true;\r
+ } //-- void setScoreOnly(boolean) \r
+\r
+ /**\r
* Sets the value of field 'sequenceRef'.\r
* \r
* @param sequenceRef the value of field 'sequenceRef'.\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _scoreOnly\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if(!target.hasScoreOnly())\r
+ return null;\r
+ return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScoreOnly();\r
+ return;\r
+ }\r
+ target.setScoreOnly( ((java.lang.Boolean)value).booleanValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _scoreOnly\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ BooleanValidator typeValidator = new BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _score\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if(!target.hasScore())\r
+ return null;\r
+ return new java.lang.Float(target.getScore());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteScore();\r
+ return;\r
+ }\r
+ target.setScore( ((java.lang.Float)value).floatValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _score\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ FloatValidator typeValidator = new FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _annotationElementList\r
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class StructureState.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class StructureState implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _visible\r
- */\r
- private boolean _visible;\r
-\r
- /**\r
- * keeps track of state for field: _visible\r
- */\r
- private boolean _has_visible;\r
-\r
- /**\r
- * Field _xpos\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public StructureState() {\r
- super();\r
- setContent("");\r
- } //-- jalview.schemabinding.version2.StructureState()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteHeight\r
- * \r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight() \r
-\r
- /**\r
- * Method deleteVisible\r
- * \r
- */\r
- public void deleteVisible()\r
- {\r
- this._has_visible= false;\r
- } //-- void deleteVisible() \r
-\r
- /**\r
- * Method deleteWidth\r
- * \r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth() \r
-\r
- /**\r
- * Method deleteXpos\r
- * \r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos() \r
-\r
- /**\r
- * Method deleteYpos\r
- * \r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos() \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight() \r
-\r
- /**\r
- * Returns the value of field 'visible'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'visible'.\r
- */\r
- public boolean getVisible()\r
- {\r
- return this._visible;\r
- } //-- boolean getVisible() \r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth() \r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos() \r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos() \r
-\r
- /**\r
- * Method hasHeight\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight() \r
-\r
- /**\r
- * Method hasVisible\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasVisible()\r
- {\r
- return this._has_visible;\r
- } //-- boolean hasVisible() \r
-\r
- /**\r
- * Method hasWidth\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
-\r
- /**\r
- * Method hasXpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
-\r
- /**\r
- * Method hasYpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int) \r
-\r
- /**\r
- * Sets the value of field 'visible'.\r
- * \r
- * @param visible the value of field 'visible'.\r
- */\r
- public void setVisible(boolean visible)\r
- {\r
- this._visible = visible;\r
- this._has_visible = true;\r
- } //-- void setVisible(boolean) \r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int) \r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int) \r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class StructureState.
+ *
+ * @version $Revision$ $Date$
+ */
+public class StructureState implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _visible
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * Field _xpos
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public StructureState() {
+ super();
+ setContent("");
+ } //-- jalview.schemabinding.version2.StructureState()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deleteHeight
+ *
+ */
+ public void deleteHeight()
+ {
+ this._has_height= false;
+ } //-- void deleteHeight()
+
+ /**
+ * Method deleteVisible
+ *
+ */
+ public void deleteVisible()
+ {
+ this._has_visible= false;
+ } //-- void deleteVisible()
+
+ /**
+ * Method deleteWidth
+ *
+ */
+ public void deleteWidth()
+ {
+ this._has_width= false;
+ } //-- void deleteWidth()
+
+ /**
+ * Method deleteXpos
+ *
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos= false;
+ } //-- void deleteXpos()
+
+ /**
+ * Method deleteYpos
+ *
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos= false;
+ } //-- void deleteYpos()
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return int
+ * @return the value of field 'height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ } //-- int getHeight()
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return boolean
+ * @return the value of field 'visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ } //-- boolean getVisible()
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return int
+ * @return the value of field 'width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ } //-- int getWidth()
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return int
+ * @return the value of field 'xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ } //-- int getXpos()
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return int
+ * @return the value of field 'ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ } //-- int getYpos()
+
+ /**
+ * Method hasHeight
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ } //-- boolean hasHeight()
+
+ /**
+ * Method hasVisible
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ } //-- boolean hasVisible()
+
+ /**
+ * Method hasWidth
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ } //-- boolean hasWidth()
+
+ /**
+ * Method hasXpos
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ } //-- boolean hasXpos()
+
+ /**
+ * Method hasYpos
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ } //-- boolean hasYpos()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ } //-- void setHeight(int)
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible the value of field 'visible'.
+ */
+ public void setVisible(boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ } //-- void setVisible(boolean)
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ } //-- void setWidth(int)
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ } //-- void setXpos(int)
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ } //-- void setYpos(int)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Object
+ */
+ public static java.lang.Object unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
+ } //-- java.lang.Object unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class StructureStateDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public StructureStateDescriptor() {\r
- super();\r
- nsURI = "www.jalview.org";\r
- xmlName = "structureState";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.xml.XMLFieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _visible\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if(!target.hasVisible())\r
- return null;\r
- return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteVisible();\r
- return;\r
- }\r
- target.setVisible( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _visible\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _xpos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if(!target.hasXpos())\r
- return null;\r
- return new java.lang.Integer(target.getXpos());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteXpos();\r
- return;\r
- }\r
- target.setXpos( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _xpos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _ypos\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if(!target.hasYpos())\r
- return null;\r
- return new java.lang.Integer(target.getYpos());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteYpos();\r
- return;\r
- }\r
- target.setYpos( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _ypos\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _width\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if(!target.hasWidth())\r
- return null;\r
- return new java.lang.Integer(target.getWidth());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteWidth();\r
- return;\r
- }\r
- target.setWidth( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _width\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _height\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- StructureState target = (StructureState) object;\r
- if(!target.hasHeight())\r
- return null;\r
- return new java.lang.Integer(target.getHeight());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- StructureState target = (StructureState) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteHeight();\r
- return;\r
- }\r
- target.setHeight( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- } );\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _height\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- jalview.schemabinding.version2.StructureStateDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return jalview.schemabinding.version2.StructureState.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class StructureStateDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field nsPrefix
+ */
+ private java.lang.String nsPrefix;
+
+ /**
+ * Field nsURI
+ */
+ private java.lang.String nsURI;
+
+ /**
+ * Field xmlName
+ */
+ private java.lang.String xmlName;
+
+ /**
+ * Field identity
+ */
+ private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public StructureStateDescriptor() {
+ super();
+ nsURI = "www.jalview.org";
+ xmlName = "structureState";
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.xml.XMLFieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ //-- _content
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
+ desc.setImmutable(true);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ return target.getContent();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ target.setContent( (java.lang.String) value);
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _content
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ StringValidator typeValidator = new StringValidator();
+ typeValidator.setWhiteSpace("preserve");
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize attribute descriptors
+
+ //-- _visible
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if(!target.hasVisible())
+ return null;
+ return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteVisible();
+ return;
+ }
+ target.setVisible( ((java.lang.Boolean)value).booleanValue());
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _visible
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ BooleanValidator typeValidator = new BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if(!target.hasXpos())
+ return null;
+ return new java.lang.Integer(target.getXpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos( ((java.lang.Integer)value).intValue());
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator= new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if(!target.hasYpos())
+ return null;
+ return new java.lang.Integer(target.getYpos());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos( ((java.lang.Integer)value).intValue());
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator= new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if(!target.hasWidth())
+ return null;
+ return new java.lang.Integer(target.getWidth());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth( ((java.lang.Integer)value).intValue());
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator= new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ StructureState target = (StructureState) object;
+ if(!target.hasHeight())
+ return null;
+ return new java.lang.Integer(target.getHeight());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ StructureState target = (StructureState) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight( ((java.lang.Integer)value).intValue());
+ }
+ catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance( java.lang.Object parent ) {
+ return null;
+ }
+ } );
+ desc.setHandler(handler);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ IntegerValidator typeValidator= new IntegerValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ } //-- jalview.schemabinding.version2.StructureStateDescriptor()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method getAccessMode
+ *
+ *
+ *
+ * @return AccessMode
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+ /**
+ * Method getExtends
+ *
+ *
+ *
+ * @return ClassDescriptor
+ */
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()
+ {
+ return null;
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+ /**
+ * Method getIdentity
+ *
+ *
+ *
+ * @return FieldDescriptor
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return identity;
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+ /**
+ * Method getJavaClass
+ *
+ *
+ *
+ * @return Class
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.StructureState.class;
+ } //-- java.lang.Class getJavaClass()
+
+ /**
+ * Method getNameSpacePrefix
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return nsPrefix;
+ } //-- java.lang.String getNameSpacePrefix()
+
+ /**
+ * Method getNameSpaceURI
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return nsURI;
+ } //-- java.lang.String getNameSpaceURI()
+
+ /**
+ * Method getValidator
+ *
+ *
+ *
+ * @return TypeValidator
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+ /**
+ * Method getXMLName
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String getXMLName()
+ {
+ return xmlName;
+ } //-- java.lang.String getXMLName()
+
+}
git://source.jalview.org / jalview.git / commitdiff