Added reaction template file option to provide custom query reaction …

…templates to editor; some minor adaptions

src/com/actelion/research/datawarrior/DataWarrior.java

@@ -40,8 +40,7 @@
 import java.awt.*;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowFocusListener;
-import java.io.File;
-import java.io.IOException;
+import java.io.*;
 import java.lang.reflect.Method;
 import java.security.CodeSource;
 import java.util.ArrayList;
@@ -62,6 +61,7 @@ public abstract class DataWarrior implements WindowFocusListener {
 	public static final String[] RESOURCE_DIR = { "Reference", "Example", "Tutorial" };
 	public static final String MACRO_DIR = "Macro";
 	public static final String PLUGIN_DIR = "Plugin";
+	public static final String QUERY_REACTION_TEMPLATE_FILE = "template/reactionqueries.txt";
 
 	private boolean mIsCapkaAvailable;
 
@@ -270,6 +270,47 @@ public void initialize() {
 		catch (Throwable t) {
 			t.printStackTrace();
 			}
+
+		initializeCustomTemplates();
+		}
+
+	private void initializeCustomTemplates() {
+		File rtf = resolveResourcePath(QUERY_REACTION_TEMPLATE_FILE);
+		if (rtf != null) {
+			try {
+				ArrayList<String[]> list = new ArrayList<>();
+				BufferedReader reader = new BufferedReader(new FileReader(rtf));
+				String[] keyAndValue = parseTemplateLine(reader);
+				if (keyAndValue != null
+				 && keyAndValue[0].equals(GenericEditorArea.TEMPLATE_TYPE_KEY)
+				 && keyAndValue[1].equals(GenericEditorArea.TEMPLATE_TYPE_REACTION_QUERIES)) {
+					keyAndValue = parseTemplateLine(reader);
+					while (keyAndValue != null) {
+						list.add(keyAndValue);
+						keyAndValue = parseTemplateLine(reader);
+					}
+				}
+				reader.close();
+				if (list.size() != 0)
+					GenericEditorArea.setReactionQueryTemplates(list.toArray(new String[0][]));
+			}
+			catch (IOException ioe) {}
+			}
+		}
+
+	private String[] parseTemplateLine(BufferedReader reader) throws IOException {
+		String line = reader.readLine();
+		if (line == null)
+			return null;
+
+		int index = line.indexOf(':');
+		if (index == -1)
+			return null;
+
+		String[] template = new String[2];
+		template[0] = line.substring(0, index).trim();
+		template[1] = line.substring(index+1).trim();
+		return template;
 		}
 
 	public void checkVersion(boolean showUpToDateMessage) {

src/com/actelion/research/datawarrior/StandardMenuBar.java

@@ -1505,7 +1505,7 @@ else if (source == jMenuFileOpenMacro)
 			else if (source == jMenuFileOpenMDLReactions)
 				new DETaskOpenMDLReactionDatabase(mApplication).defineAndRun();
 			else if (source == jMenuFileMerge)
-				new DETaskMergeFile(mParentFrame, true).defineAndRun();
+				new DETaskMergeFile(mParentFrame).defineAndRun();
 			else if (source == jMenuFileAppend) {
 				if (mParentFrame.getTableModel().getTotalRowCount() == 0)
 					JOptionPane.showMessageDialog(mParentFrame, "You cannot append a file to an empty table. Use 'Open File...' instead.");

src/com/actelion/research/datawarrior/task/StandardTaskFactory.java

@@ -180,7 +180,7 @@ public AbstractTask createTaskFromCode(DEFrame frame, String taskCode) {
 			 : codeMatches(taskCode, DETaskJumpToReferenceRow.TASK_NAME) ? new DETaskJumpToReferenceRow(frame, mainPane)
 			 : codeMatches(taskCode, DETaskMapReactions.TASK_NAME) ? new DETaskMapReactions(frame)
 			 : codeMatches(taskCode, DETaskMergeColumns.TASK_NAME) ? new DETaskMergeColumns(frame)
-			 : codeMatches(taskCode, DETaskMergeFile.TASK_NAME) ? new DETaskMergeFile(frame, false)
+			 : codeMatches(taskCode, DETaskMergeFile.TASK_NAME) ? new DETaskMergeFile(frame)
 			 : codeMatches(taskCode, DETaskNew2DView.TASK_NAME) ? new DETaskNew2DView(frame, mainPane,null)
 			 : codeMatches(taskCode, DETaskNew3DView.TASK_NAME) ? new DETaskNew3DView(frame, mainPane,null)
 			 : codeMatches(taskCode, DETaskNewCardsView.TASK_NAME) ? new DETaskNewCardsView(frame, mainPane,null)

src/com/actelion/research/datawarrior/task/chem/DETaskAdd3DCoordinates.java

@@ -756,7 +756,7 @@ private void addConformersToQueue(int row, StereoMolecule mol) throws Exception
 		if (mLargestFragmentOnly) {
 			mol.stripSmallFragments();
 			if (mNeutralizeLargestFragment)
-				new MoleculeNeutralizer().neutralizeChargedMolecule(mol);
+				MoleculeNeutralizer.neutralizeChargedMolecule(mol);
 			}
 
 		// don't create any protonation states

src/com/actelion/research/datawarrior/task/chem/DETaskAddLargestFragment.java

@@ -179,7 +179,7 @@ public void processRow(int row, int firstNewColumn, StereoMolecule containerMol,
 	private void handleMolecule(StereoMolecule mol) {
 		mol.stripSmallFragments();
 		if (mNeutralizeFragment)
-			new MoleculeNeutralizer().neutralizeChargedMolecule(mol);
+			MoleculeNeutralizer.neutralizeChargedMolecule(mol);
 		if (mAsSubstructure)
 			mol.setFragment(true);
 		}

src/com/actelion/research/datawarrior/task/chem/DETaskDockIntoProteinCavity.java

@@ -233,7 +233,7 @@ public void processRow(int row, int firstNewColumn, StereoMolecule containerMol,
 	private void handleMolecule(StereoMolecule mol) {
 		mol.stripSmallFragments();
 		if (mProtonateFragment) {
-			new MoleculeNeutralizer().neutralizeChargedMolecule(mol);
+			MoleculeNeutralizer.neutralizeChargedMolecule(mol);
 			assignLikelyProtonationStates(mol);
 			}
 

src/com/actelion/research/datawarrior/task/file/DETaskMergeFile.java

@@ -41,7 +41,7 @@ public class DETaskMergeFile extends AbstractTask implements TaskConstantsMergeF
 	private UIDelegateMergeFile	mUIDelegate;
 	private CompoundTableLoader	mLoader;
 
-	public DETaskMergeFile(DEFrame parent, boolean isInteractive) {
+	public DETaskMergeFile(DEFrame parent) {
 		super(parent, true);
 		// All tasks that use CompoundTableLoader need to run in an own thread if they run in a macro
 		// to prevent the CompoundTableLoader to run processData() in a new thread without waiting