Creates the new string matrix. Improves and implement the usage of th…

…e new matrix in the matrix editor and the matrix manager.

plugins/net.bioclipse.statistics.business/src/net/bioclipse/statistics/business/business/IMatrixManager.java

@@ -13,7 +13,9 @@
 import java.lang.reflect.InvocationTargetException;
 import java.util.List;
 
+import org.eclipse.core.resources.IFile;
 import org.eclipse.core.runtime.CoreException;
+import org.eclipse.jface.bindings.keys.ParseException;
 
 import net.bioclipse.core.PublishedClass;
 import net.bioclipse.core.PublishedMethod;
@@ -44,6 +46,20 @@ public IMatrixResource create(
     )
     public IMatrixResource create(double[][] values);
 
+    @Recorded
+    @PublishedMethod(methodSummary=
+        "Creates a new matrix domain object, starting from a array of " +
+        "String arrays."
+    )
+    public IMatrixResource create(String[][] values);
+
+    @Recorded
+    @PublishedMethod(methodSummary=
+        "Creates a new matrix domain object, from a file."
+    )
+    public IMatrixResource create(IFile file) throws ParseException;
+    public IMatrixResource create(String file) throws ParseException;
+
     @Recorded
     @PublishedMethod(methodSummary=
         "Creates a new, empty matrix domain object."
@@ -57,7 +73,7 @@ public IMatrixResource create(
     		"when the number of values is incompatible with the number of columns " +
     		"of the existing matrix." 
     )
-    public IMatrixResource addRow(IMatrixResource matrix, List<Double> values)
+    public IMatrixResource addRow(IMatrixResource matrix, List<String> values)
     throws BioclipseException;
 
     @Recorded

plugins/net.bioclipse.statistics.business/src/net/bioclipse/statistics/business/business/MatrixManager.java

@@ -25,7 +25,9 @@
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.NullProgressMonitor;
+import org.eclipse.jface.bindings.keys.ParseException;
 import org.eclipse.ui.IFileEditorInput;
+import org.eclipse.ui.part.FileEditorInput;
 
 public class MatrixManager implements IBioclipseManager {
 
@@ -37,6 +39,19 @@ public String getManagerName() {
         return "matrix";
     }
 
+    public IMatrixResource create( IFile file ) throws ParseException {
+        String name = file.getName();
+        IFileEditorInput fei = new FileEditorInput( file );
+        IMatrixResource matrix =
+                new MatrixResource(name, fei);
+
+        if (!matrix.parseResource())
+            throw new ParseException( "Could not parse " + 
+                    file.getFullPath().toOSString() + " into an matrix." );
+
+        return matrix;
+    }
+
     public IMatrixResource create(
             String valueSequence, int ncol) {
         StringTokenizer tokenizer = new StringTokenizer(valueSequence);
@@ -51,15 +66,17 @@ public IMatrixResource create(
         int rowCount = 0;
         int colCount = 0;
         while (tokenizer.hasMoreTokens()) {
-            double value = Double.NaN;
-            try {
-                value = Double.parseDouble(tokenizer.nextToken());
-            } catch (NumberFormatException exception) {}
-            try {
-                matrix.set(rowCount+1, colCount+1, value);
-            } catch (Exception exception) {
-                exception.printStackTrace();
-            }
+            String value = tokenizer.nextToken();
+            matrix.set(rowCount+1, colCount+1, value);
+//            double value = Double.NaN;
+//            try {
+//                value = Double.parseDouble(tokenizer.nextToken());
+//            } catch (NumberFormatException exception) {}
+//            try {
+//                matrix.set(rowCount+1, colCount+1, value);
+//            } catch (Exception exception) {
+//                exception.printStackTrace();
+//            }
             colCount++;
             if (colCount == ncol) {
                 colCount = 0;
@@ -84,6 +101,21 @@ public IMatrixResource create(double[][] values) {
         }
         return matrix;
     }
+
+    public IMatrixResource create(String[][] values) {
+        IMatrixResource matrix =
+            new MatrixResource("", (IFileEditorInput)null);
+        int ncol = values.length;
+        int nrow = values[0].length;
+        matrix.setSize(ncol, nrow);
+
+        for (int row=0; row<nrow; row++) {
+            for (int col=0; col<ncol; col++) {
+                matrix.set(row+1, col+1, values[row][col]);
+            }
+        }
+        return matrix;
+    }
 
     public void setColumnLabels(IMatrixResource matrix, String[] names) {
         int col = 1;
@@ -107,7 +139,7 @@ public IMatrixResource empty() {
         return matrix;
     }
 
-    public IMatrixResource addRow(IMatrixResource matrix, List<Double> values)
+    public IMatrixResource addRow(IMatrixResource matrix, List<String> values)
     throws BioclipseException {
     	int row = matrix.getRowCount();
     	if (row != 0 && values.size() != matrix.getColumnCount())

plugins/net.bioclipse.statistics.jama/src/net/bioclipse/model/JamaMatrix.java

@@ -13,6 +13,8 @@
 
 import java.util.ArrayList;
 
+import org.apache.log4j.Logger;
+
 import net.bioclipse.statistics.model.IMatrixImplementationResource;
 import net.bioclipse.statistics.model.MatrixImplementationResource;
 
@@ -23,6 +25,7 @@ public class JamaMatrix extends MatrixImplementationResource {
 	private Matrix matrix = null;
 	private boolean hasRowHeader, hasColHeader, hasResponseColumn;
 	private int responseColumnIndex;
+	private Logger logger = Logger.getLogger( this.getClass() );
 
 	//Column and row headers
 	private ArrayList<String> colIds;
@@ -40,15 +43,15 @@ private JamaMatrix(int rows, int cols) {
     responseColumn = new ArrayList<String>(rows);
 	}
 
-	public double get(int row, int col) throws Exception {
+	public String get(int row, int col) throws Exception {
 		if (row > getRowCount()) 
 			throw new ArrayIndexOutOfBoundsException("Matrix does not have so many rows!");
 		if (col > getColumnCount()) 
 			throw new ArrayIndexOutOfBoundsException("Matrix does not have so many columns!");
 
-		return matrix.get(row-1, col-1);
+		return Double.toString( matrix.get(row-1, col-1) );
 	}
-
+	
 	public void set(int row, int col, double value) throws Exception {
 		if (row < 1)
 			throw new ArrayIndexOutOfBoundsException(
@@ -72,6 +75,16 @@ public void set(int row, int col, double value) throws Exception {
 		matrix.set(row-1, col-1, value);
 	}
 
+	public void set(int row, int col, String value) throws Exception {
+	    try {
+	        double val = Double.parseDouble( value );
+	        this.set( row, col, val );
+	    } catch (NumberFormatException e) {
+	        throw new NumberFormatException( "The JamaMatrix can only handle " +
+	        		"numbers" );
+	    }
+	}
+
 	public int getColumnCount() throws Exception {
 		return matrix.getColumnDimension();
 	}
@@ -104,7 +117,14 @@ public IMatrixImplementationResource getInstance(int rows, int cols, int respons
 //	     newInstance.responseColumn=this.responseColumn;
 	     return newInstance;
 	   }
-
+
+	 public IMatrixImplementationResource getInstance( int rows, int cols, 
+	                                                      boolean lowerTriangular, 
+	                                                      boolean symmetric ) {
+	     logger.warn( "The jama matrix do not handle triangular matrixes, " +
+	     		"returning an ordinary" );
+	     return getInstance( rows, cols );
+	 }
 	public String getRowName( int index ) {
 		if( !rowIds.isEmpty() && index<=rowIds.size())
 			return rowIds.get(index-1);

plugins/net.bioclipse.statistics/META-INF/MANIFEST.MF

@@ -25,5 +25,6 @@ Export-Package: net.bioclipse.statistics,
 Bundle-Activator: net.bioclipse.statistics.Activator
 Bundle-ClassPath: .,
  jars/org.eclipse.nebula.widgets.grid_1.0.0.jar
-Import-Package: org.apache.log4j
+Import-Package: net.bioclipse.ui.business.describer,
+ org.apache.log4j
 Bundle-RequiredExecutionEnvironment: J2SE-1.5

plugins/net.bioclipse.statistics/plugin.xml

@@ -62,5 +62,38 @@
             priority="normal">
       </content-type>
    </extension>
+   <extension
+         point="net.bioclipse.ui.bioobjectDescriber">
+      <BioObject
+            describer="net.bioclipse.statistics.describer.MatrixResourceDescriber"
+            id="net.bioclipse.statistics.describer"
+            objectClass="net.bioclipse.statistics.model.IMatrixResource">
+      </BioObject>
+   </extension>
+   <extension
+         point="org.eclipse.ui.editorActions">
+      <editorContribution
+            id="net.bioclipse.statistics.matrixEditorContribution"
+            targetID="net.bioclipse.editors.MatrixGridEditor">
+         <action
+               class="net.bioclipse.statistics.RowHeaderDelegate"
+               icon="icons/RowHeader.gif"
+               id="net.bioclipse.statistics.rowHeaderAction"
+               label="Row header"
+               style="toggle"
+               toolbarPath="IWorkbenchActionConstants.MB_ADDITIONS"
+               tooltip="Add / remove row headers">
+         </action>
+         <action
+               class="net.bioclipse.statistics.ColHeaderDelegate"
+               icon="icons/ColHeader.gif"
+               id="net.bioclipse.statistics.colHeaderAction"
+               label="Column header"
+               style="toggle"
+               toolbarPath="IWorkbenchActionConstants.MB_ADDITIONS"
+               tooltip="Add / remove column headers">
+         </action>
+      </editorContribution>
+   </extension>
 
 </plugin>

plugins/net.bioclipse.statistics/src/net/bioclipse/statistics/ColHeaderDelegate.java

@@ -0,0 +1,40 @@
+package net.bioclipse.statistics;
+
+import net.bioclipse.statistics.editors.MatrixEditor;
+
+import org.eclipse.jface.action.IAction;
+import org.eclipse.jface.viewers.ISelection;
+import org.eclipse.ui.IEditorActionDelegate;
+import org.eclipse.ui.IEditorPart;
+
+/**
+ * Handles the column-header toggle-button.
+ * 
+ * @author Klas Jšnsson (klas.joensson@gmail.com)
+ *
+ */
+public class ColHeaderDelegate implements IEditorActionDelegate {
+
+    private IEditorPart targetPart;
+
+    public void run( IAction action ) {
+        if (targetPart != null && action != null) 
+            if (targetPart instanceof MatrixEditor) 
+                action.setChecked( ((MatrixEditor) targetPart).runColumnHeaderAction() );
+
+    }
+
+    public void selectionChanged( IAction action, ISelection selection ) {
+        if (targetPart instanceof MatrixEditor) 
+            action.setChecked( ((MatrixEditor) targetPart).hasColumnHeader() );
+    }
+
+    public void setActiveEditor( IAction action, IEditorPart targetEditor ) {
+        targetPart = targetEditor;
+        if (targetPart instanceof MatrixEditor) {
+            action.setChecked( ((MatrixEditor) targetPart).hasColumnHeader() );
+            ((MatrixEditor) targetPart).addActionDelegate( this );
+        }
+    }
+
+}

plugins/net.bioclipse.statistics/src/net/bioclipse/statistics/RowHeaderDelegate.java

@@ -0,0 +1,44 @@
+package net.bioclipse.statistics;
+
+import net.bioclipse.statistics.editors.MatrixEditor;
+
+import org.eclipse.jface.action.IAction;
+import org.eclipse.jface.viewers.ISelection;
+import org.eclipse.ui.IEditorActionDelegate;
+import org.eclipse.ui.IEditorPart;
+
+/**
+ * Handles the row-header toggle-button.
+ * 
+ * @author Klas Jšnsson (klas.joensson@gmail.com)
+ *
+ */
+public class RowHeaderDelegate implements IEditorActionDelegate {
+
+    private IEditorPart targetPart;
+
+    public void run( IAction action ) {
+        if (targetPart != null && action != null) {
+            if (targetPart instanceof MatrixEditor)
+                action.setChecked( ((MatrixEditor) targetPart).runRowHeaderAction() );
+        }
+
+    }
+
+    public void selectionChanged( IAction action, ISelection selection ) {
+        if (targetPart instanceof MatrixEditor) {
+            action.setChecked( ((MatrixEditor) targetPart).hasRowHeader() );
+
+        }
+    }
+
+    public void setActiveEditor( IAction action, IEditorPart targetEditor ) {
+        targetPart = targetEditor;
+        if (targetPart instanceof MatrixEditor) {
+            action.setChecked( ((MatrixEditor) targetPart).hasRowHeader() );
+            ((MatrixEditor) targetPart).addActionDelegate( this );
+        }
+
+    }
+
+}

plugins/net.bioclipse.statistics/src/net/bioclipse/statistics/describer/MatrixResourceDescriber.java

@@ -0,0 +1,28 @@
+package net.bioclipse.statistics.describer;
+
+import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.statistics.model.IMatrixResource;
+import net.bioclipse.ui.business.describer.IBioObjectDescriber;
+
+
+public class MatrixResourceDescriber implements IBioObjectDescriber {
+
+    public MatrixResourceDescriber() {
+
+    }
+
+    public String getPreferredEditorID( IBioObject object )
+                                                           throws BioclipseException {
+
+        if (object instanceof IMatrixResource) {
+            String [] possibleEditorIDs = 
+                    ((IMatrixResource) object).getEditorIDs();
+            /* Let's assume that the first in the array is the one that is 
+             * preferred.*/
+            return possibleEditorIDs[0];
+        }
+        return null;
+    }
+
+}