/*
Copyright (c) 2009 The Regents of the University of California.
All rights reserved.
Permission is hereby granted, without written agreement and without
license or royalty fees, to use, copy, modify, and distribute this
software and its documentation for any purpose, provided that the above
copyright notice and the following two paragraphs appear in all copies
of this software.
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
ENHANCEMENTS, OR MODIFICATIONS..
*/
package org.clothocad.tool.bulltrowell.interpreters;
import java.awt.Color;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.SwingUtilities;
import org.clothocad.tool.bulltrowell.view.hub;
import org.clothocore.api.core.Collector;
import org.clothocore.api.data.Collection;
import org.clothocore.api.data.Feature;
import org.clothocore.api.data.Format;
import org.clothocore.api.data.ObjLink;
import org.clothocore.api.data.ObjType;
import org.clothocore.api.data.Person;
import org.clothocad.tool.bulltrowell.view.spreadsheet;
/**
*
* @authorInputString J. Christopher Anderson
*/
public class addFeature implements interpreter {
public addFeature() {
String[] titles = { "Nickname", "Sequence", "Author", "Family", "Risk Group", "Forward Color", "Reverse Color" };
_numCols = titles.length;
_numRows = hub.numrows;
_data = new String[_numRows][_numCols];
for(int i=0; i<_numRows; i++) {
for(int j=0; j< _numCols; j++) {
_data[i][j] = "";
}
}
_mySheet = new spreadsheet(_data, titles, this);
_mySheet.setTitle("Add Features");
_mySheet.setTitleArea("Add features from Excel by Copy and Paste<br>You must supply name and sequence. Other fields are optional.<br> For coding sequences, enter sequence as ATG...TAA, Feature Type is CDS (or ORF).");
if(Collector.isConnected()) {
loadingthread = new Thread() {
@Override
public void run() {
//Get the current user
final Person user = Collector.getCurrentUser();
//Put in the authorInputString chooser (field 2)
_persons = Collector.getAllLinksOf(ObjType.PERSON);
final Object[] authorChoices = _persons.toArray();
try {
SwingUtilities.invokeAndWait(new Runnable() {
@Override
public void run() {
_mySheet.putComboField2("Author", authorChoices, user.getObjLink());
}
});
} catch (InterruptedException ex) {
Logger.getLogger(addFeature.class.getName()).log(Level.SEVERE, null, ex);
} catch (InvocationTargetException ex) {
Logger.getLogger(addFeature.class.getName()).log(Level.SEVERE, null, ex);
}
}
};
loadingthread.start();
}
}
@Override
public void receiveData(Object[][] data) {
_data = (String[][]) data;
for(int i=0; i<_data.length; i++) {
for(int j=0; j<_data[0].length; j++) {
System.out.print(_data[i][j] + "");
}
System.out.println("");
}
//Create a new Collection to store everything
if(_outCollection==null) {
_outCollection = new Collection();
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
_outCollection.launchDefaultViewer();
}
});
}
//If it's still loading wait for it to finish loading
try {
loadingthread.join();
} catch (InterruptedException ex) {
}
//Get the formatInputString and authorInputString defaults
ObjLink link = (ObjLink) _mySheet.getComboField2();
_defaultAuthor = Collector.getPerson(link.uuid);
_data = (String[][]) data;
for(int i=0; i<_data.length; i++) {
try {
//Retrieve the data in the current line
String name = _data[i][0];
String seq = _data[i][1];
//If any of the 2 required fields weren't entered, abort this line
if(name.equals("") || seq.equals("")) {
continue;
}
//Retrieve any additional lines entered
String authorInputString = _data[i][2];
String familyString = _data[i][3];
String riskgroup = _data[i][4];
String forcolor = _data[i][5];
String revcolor = _data[i][6];
//If an authorInputString was typed in, search for that Person
Person featureAuthor;
if(authorInputString.equals("")) {
featureAuthor = _defaultAuthor;
} else {
featureAuthor = Person.retrieveByName(authorInputString);
if(featureAuthor==null) {
continue;
}
}
boolean isCDS = false;
if(familyString.toUpperCase().equals("CDS") || familyString.toUpperCase().equals("ORF") || familyString.toUpperCase().equals("PROTEIN")) {
isCDS = true;
}
Feature newfeature = Feature.generateFeature(name, seq, featureAuthor, isCDS);
newfeature.changeAuthor(featureAuthor);
Color forwardColor = null;
Color reverseColor = null;
if(newfeature!=null) {
//Try to parse the colors
try {
forwardColor = new Color(Integer.parseInt(forcolor));
System.out.println("Setting forward color from parseInt");
} catch(NumberFormatException e) {
}
if(forwardColor==null) {
if(forcolor.startsWith("#") && forcolor.length() > 5) {
String temp = forcolor.substring(1);
forcolor = temp;
}
try {
forwardColor = new Color(Integer.parseInt( forcolor, 16 ));
System.out.println("Setting forward color from hexadecimal");
} catch(NumberFormatException e) {
System.out.println("rejecting forward color");
}
}
if(forwardColor==null) {
forwardColor = HTMLColors.decodeColor(forcolor);
if(forwardColor!=null) {
System.out.println("Setting forward color from html parser");
}
}
try {
reverseColor = new Color(Integer.parseInt(revcolor));
} catch(NumberFormatException e) {
}
if(reverseColor==null) {
if(revcolor.startsWith("#") && revcolor.length() > 5) {
String temp = revcolor.substring(1);
revcolor = temp;
}
try {
reverseColor = new Color(Integer.parseInt( revcolor, 16 ));
} catch(NumberFormatException e) {
System.out.println("rejecting forward color");
}
}
if(reverseColor==null) {
reverseColor = HTMLColors.decodeColor(revcolor);
}
//If Color got parsed, set the colors
if(forwardColor!=null) {
newfeature.changeForwardColor(forwardColor);
}
if(reverseColor!=null) {
newfeature.changeReverseColor(reverseColor);
}
//Set the risk group
try {
newfeature.changeRiskGroup((short) Integer.parseInt(riskgroup));
} catch(NumberFormatException e) {
}
}
//Notify user that the Feature was created
_mySheet.appendLogMessage(newfeature.getName() + "\n");
System.out.println("I created feature " + newfeature.getName());
_outCollection.addObject(newfeature);
//Clear the data in the data table
for(int col=0; col<_numCols; col++) {
_data[i][col] = "";
}
} catch(Exception e) {
continue;
}
}
_mySheet.refreshData(_data);
}
/*-----------------
variables
-----------------*/
private String[][] _data;
private spreadsheet _mySheet;
private ArrayList<ObjLink> _persons;
private ArrayList<ObjLink> _collections;
private ArrayList<ObjLink> _formats;
private Person _defaultAuthor;
private Collection _outCollection;
private Format _defaultFormat;
private int _numCols;
private int _numRows;
private String messageText="";
private Thread loadingthread;
}