Merge branch 'master' of https://github.com/Bio7/Bio7

com.eco.bio7.javaedit/build.properties

@@ -11,10 +11,9 @@ bin.includes = plugin.xml,\
                .classpath,\
                com/,\
                epl-v10.html,\
-               libs/,\
                .,\
                icons/,\
-               libs/commons-compiler-3.0.7.jar
+               libs/
 src.includes = .classpath,\
                META-INF/,\
                about.html,\

com.eco.bio7.markdownedit/build.properties

@@ -9,6 +9,4 @@ bin.includes = plugin.xml,\
                build.properties,\
                .settings/,\
                .classpath,\
-               libs/,\
-               libs/flexmark-all-0.28.6-lib.jar,\
-               libs/autolink-0.7.0.jar
+               libs/

com.eco.bio7/plugin.xml

@@ -531,7 +531,7 @@
       <keyBinding
             commandId="com.eco.bio7.save_r_workspace2"
             keyConfigurationId="org.eclipse.ui.defaultAcceleratorConfiguration"
-            keySequence="CTRL+ALT+SHIFT+O">
+            keySequence="CTRL+ALT+K">
       </keyBinding>
       <command
             description="Open the R preferences"

com.eco.bio7/src/com/eco/bio7/preferences/RServePrefs.java

@@ -121,6 +121,9 @@ public void widgetSelected(final SelectionEvent e) {
 
 		addField(new StringFieldEditor("RSHELL_ACTIVATION_CHARS", "Activation chars (Restart to apply!)", -1, StringFieldEditor.VALIDATE_ON_KEY_STROKE, getFieldEditorParent()));
 		addField(new StringFieldEditor("RSHELL_SEPERATOR_CHARS", "Seperator chars", -1, StringFieldEditor.VALIDATE_ON_KEY_STROKE, getFieldEditorParent()));
+		addField(new RadioGroupFieldEditor("RSHELL_CODE_COMPLETION_ACTIVATOR_ALTERED", "Use a different key combination for code completion activation", 3, new String[][]{{"Strg+Space", "STRG"}, {"Alt+Space", "ALT"},{"Cmd+Space", "CMD"}}, getFieldEditorParent(), false));
+		//addField(new BooleanFieldEditor("RSHELL_CODE_COMPLETION_ACTIVATOR_ALTERED", "Use Key Combination 'ALT+SPACE' to trigger code completion (Restart to apply!)", getFieldEditorParent()));
+
 		{
 			LabelFieldEditor labelFieldEditor = new LabelFieldEditor("Close and reopen R-Shell view or restart necessary:", getFieldEditorParent());
 			labelFieldEditor.setLabelText("Code Completion Popup");

com.eco.bio7/src/com/eco/bio7/rbridge/RShellView.java

@@ -425,7 +425,7 @@ public void keyPressed(KeyEvent e) {
 
 				if (ApplicationWorkbenchWindowAdvisor.getOS().equals("Mac")) {
 
-					if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.ALT) == SWT.ALT && (e.keyCode == 'r')) {
+					if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.stateMask & SWT.ALT) == SWT.ALT && (e.keyCode == 'r')) {
 
 						/*
 						 * Add code completion to textfield! At startup load the default R proposals and
@@ -434,7 +434,7 @@ public void keyPressed(KeyEvent e) {
 						 */
 						if (RServe.isAliveDialog()) {
 							shellCompletion.update();
-							System.out.println("Reloaded code completion!");
+							System.out.println("\nReloaded code completion!");
 
 						}
 
@@ -445,7 +445,6 @@ public void keyPressed(KeyEvent e) {
 						 */
 						IDocument doc = new Document();
 						new OpenFileCreateSourceTemplate(doc, 0, doc.getLength());
-						String t = text.getText();
 						// String a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						text.insert(doc.get());
@@ -456,20 +455,18 @@ else if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.SHIF
 						IDocument doc = new Document();
 						new SaveFileCreateSourceTemplate(doc, 0, doc.getLength());
 						text.insert(doc.get());
-					} else if (((e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == '-')) {
-						String t = text.getText();
+					} else if ((((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == 'b')) {
 						// String a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						// text.setText(a + "<-" + b);
 						text.insert("<");
 						text.insert("-");
-					} else if (((e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == 'n')) {
-						String t = text.getText();
+					} else if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && ((e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == 'n')) {
 						// String a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						// text.setText(a + "<-" + b);
 						text.insert(" %>% ");
-					} else if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == 'i')) {
+					} else if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.stateMask & SWT.ALT) == SWT.ALT && (e.keyCode == 'i')) {
 						setTextInREditor();
 					}
 
@@ -494,7 +491,6 @@ else if (((e.stateMask & SWT.COMMAND) == SWT.COMMAND) && (e.stateMask & SWT.SHIF
 						 */
 						IDocument doc = new Document();
 						new OpenFileCreateSourceTemplate(doc, 0, doc.getLength());
-						String t = text.getText();
 						// a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						text.insert(doc.get());
@@ -506,14 +502,12 @@ else if (((e.stateMask & SWT.CTRL) == SWT.CTRL) && (e.stateMask & SWT.SHIFT) ==
 						new SaveFileCreateSourceTemplate(doc, 0, doc.getLength());
 						text.insert(doc.get());
 					} else if (((e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == '-')) {
-						String t = text.getText();
 						// String a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						// text.setText(a + "<-" + b);
 						text.insert("<-");
 
 					} else if (((e.stateMask & SWT.ALT) == SWT.ALT) && (e.stateMask & SWT.SHIFT) == SWT.SHIFT && (e.keyCode == 'n')) {
-						String t = text.getText();
 						// String a = t.substring(0, text.getCaretPosition());
 						// String b = t.substring(text.getCaretPosition(), t.length());
 						// text.setText(a + "<-" + b);
@@ -1231,17 +1225,31 @@ public void widgetSelected(final SelectionEvent e) {
 			public void widgetSelected(final SelectionEvent e) {
 				ToolTip infoTip = new ToolTip(new Shell(), SWT.BALLOON | SWT.ICON_INFORMATION);
 				infoTip.setText("Info!");
-
-				infoTip.setMessage("Expression textfield:" + "_________________________________\n" + "STRG + SPACE = Open code completion!\n"+ "ESC =  Close code completion!\n"+ "UP ARROW =  Open history!\n"
-						+ "STRG(CMD) + SHIFT + I = Transfer history to opened R editor!\n" + "STRG(CMD) + ALT + R = Refresh code completion!\n" + "STRG(CMD) + SHIFT + ALT + O = Open file and create load file template!\n"
-						+ "STRG(CMD) + SHIFT + ALT + S = Save file and create save file template!\n" + "SHIFT + ALT + - = Create assign operator ('<-')!\n"
-						+ "SHIFT + ALT + N = Create pipe operator ('%>%')!\n" + "Key + Mouse Click (before bracket) - select matching brackets!\n\n" + "Objects panel (left):"
-						+ "_________________________________\n" + "Selection + 'C' key = Concatenate selected variables in Expression textfield!\n"
-						+ "Selection + 'A' key = Comma seperate selected variables in Expression textfield!\n" + "Right-Click = Menu\n"
-						+ "Select variable(s) = To show, summarize, plot, transfer and convert data!\n\n" + "Tabs templates:" + "_________________________________\n"
+				if (ApplicationWorkbenchWindowAdvisor.getOS().equals("Mac")) {
+					infoTip.setMessage("Expression textfield:\n\n"  + "STRG + SPACE (Change in pref.!) = Open code completion!\n" + "ESC =  Close code completion!\n"
+							+ "UP ARROW =  Open history!\n" + "CMD + ALT + SHIFT + I = Transfer history to opened R editor!\n" + "CMD + ALT + SHIFT + R = Refresh code completion!\n"
+							+ "CMD + ALT + SHIFT + O = Open file and create load file template!\n" + "CMD + ALT + SHIFT + S = Save file and create save file template!\n"
+							+ "CMD + ALT + SHIFT + B = Create assign operator ('<-')!\n" + "CMD + ALT + SHIFT + N = Create pipe operator ('%>%')!\n"
+							+ "Key + Mouse Click (before bracket) - select matching brackets!\n\n" + "Objects panel (left):\n\n"
+							+ "Selection + 'C' key = Concatenate selected variables in Expression textfield!\n" + "Selection + 'A' key = Comma seperate selected variables in Expression textfield!\n"
+							+ "Right-Click = Menu\n" + "Select variable(s) = To show, summarize, plot, transfer and convert data!\n\n" + "Tabs templates:\n\n"
+							+ "Double-Click = Add template to the R-Shell textfield!\n" + "Double-Right-Click = Add template to the R editor!\n"
+
+					);
+
+				}
+				else {
+				infoTip.setMessage("Expression textfield:\n\n" + "STRG + SPACE (Change in pref.!) = Open code completion!\n" + "ESC =  Close code completion!\n"
+						+ "UP ARROW =  Open history!\n" + "STRG + SHIFT + I = Transfer history to opened R editor!\n" + "STRG + ALT + R = Refresh code completion!\n"
+						+ "STRG + SHIFT + ALT + O = Open file and create load file template!\n" + "STRG + SHIFT + ALT + S = Save file and create save file template!\n"
+						+ "SHIFT + ALT + - = Create assign operator ('<-')!\n" + "SHIFT + ALT + N = Create pipe operator ('%>%')!\n"
+						+ "Key + Mouse Click (before bracket) - select matching brackets!\n\n" + "Objects panel (left):\n\n"
+						+ "Selection + 'C' key = Concatenate selected variables in Expression textfield!\n" + "Selection + 'A' key = Comma seperate selected variables in Expression textfield!\n"
+						+ "Right-Click = Menu\n" + "Select variable(s) = To show, summarize, plot, transfer and convert data!\n\n" + "Tabs templates:\n\n"
 						+ "Double-Click = Add template to the R-Shell textfield!\n" + "Double-Right-Click = Add template to the R editor!\n"
 
 				);
+				}
 				infoTip.setVisible(true);
 
 			}

com.eco.bio7/src/com/eco/bio7/rbridge/UpdateRPackagesJob.java

@@ -50,7 +50,7 @@ public IStatus runInWorkspace(IProgressMonitor monitor) {
 			/* If a location is given! */
 
 			// destdir = destdir.replace("\\", "\\\\");
-
+            /*Here we update the packages but exclude Rserve!*/
 			String out = null;
 			try {
 				out = c.eval(".pkgListToUpdate <- installed.packages(priority='NA')[,'Package'];" + ".pkgListToUpdate<-.pkgListToUpdate[-which(.pkgListToUpdate==\"Rserve\",arr.ind =TRUE)];"

com.eco.bio7/src/com/eco/bio7/rbridge/completion/ShellCompletion.java

@@ -99,15 +99,28 @@ static char[] getAutoactivationChars() {
 		String allChars = LCL;
 		return allChars.toCharArray();
 	}
-
 
 	static KeyStroke getActivationKeystroke() {
-		KeyStroke instance = KeyStroke.getInstance(new Integer(SWT.CTRL).intValue(), new Integer(' ').intValue());
+		IPreferenceStore storeLocal = Bio7Plugin.getDefault().getPreferenceStore();
+		KeyStroke instance;
+		String useAlt = storeLocal.getString("RSHELL_CODE_COMPLETION_ACTIVATOR_ALTERED");
+		if (useAlt.equals("CMD")) {
+			instance = KeyStroke.getInstance(new Integer(SWT.COMMAND).intValue(), new Integer(' ').intValue());
+		}
+
+		else if (useAlt.equals("ALT")) {
+			instance = KeyStroke.getInstance(new Integer(SWT.ALT).intValue(), new Integer(' ').intValue());
+		}
+
+		else {
+			instance = KeyStroke.getInstance(new Integer(SWT.CTRL).intValue(), new Integer(' ').intValue());
+		}
+
 		return instance;
 	}
 
 	public ShellCompletion(RShellView view, Text control, final IControlContentAdapter controlContentAdapter) {
-		//IPreferenceStore store = Bio7Plugin.getDefault().getPreferenceStore();
+		// IPreferenceStore store = Bio7Plugin.getDefault().getPreferenceStore();
 		this.view = view;
 		this.control = control;
 		contentProposalProvider = new ContentProposalProvider();

com.eco.bio7/src/com/eco/bio7/rcp/ApplicationWorkbenchWindowAdvisor.java

@@ -638,6 +638,7 @@ public void perspectiveSavedAs(IWorkbenchPage page, IPerspectiveDescriptor oldPe
 		store.setDefault("RSHELL_SEPERATOR_CHARS", ";(,[=-+ ");
 		store.setDefault("CODE_COMPLETION_POPUP_SIZE_X",600);
 		store.setDefault("CODE_COMPLETION_POPUP_SIZE_Y",400);
+		store.setDefault("RSHELL_CODE_COMPLETION_ACTIVATOR_ALTERED","STRG");
 
 		store.setDefault("LATEX_CLEAN_FILES", false);