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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
import java.util.HashMap;
import java.util.Iterator;
import java.io.File;
import java.util.Calendar;
import java.util.Date;
/**
* The main class of ProAlign, the probabilistic alignment program.
*/
public class ProAlign {
public static double modelDelta = 0.1d; // HMM
public static double modelEpsilon = 0.75d; // HMM
public static double distScale = 1d; // distance scale factor
public static double gapFreq = 0.05d; // prot model gap freq
public static double gapProb = 0.001d; // prot model gap subst prob
public int pwDnaOpen = 1500; // pw alignment
public int pwDnaExt = 700; // pw alignment
public int pwProtOpen = 1000; // pw alignment
public int pwProtExt = 100; // pw alignment
public String pwProtMatrix = "pam120"; // pw alignment
public String treefile = new String();
public String seqfile;
public String outfile = new String("proalign.out");
public boolean nogui = false;
public boolean doTree = false;
boolean isAligned = false;
public int outformat = 2;
int nodeNumber = -1;
int defBandWidth;
int defOffset;
HashMap seqs;
public static boolean isDna = true;
static boolean isResultWindow = false;
public static boolean trackBest = true; // traceback best
static boolean DEBUG = true; // write log
public static boolean removeTrailing = true;
public static boolean penalizeTerminal = true;
public static boolean correctMultiple = true;
public static boolean writeMin = true;
public static boolean writeMean = false;
public static boolean writeAll = false;
public static boolean writeRoot = false;
public static boolean estimateGapFreq = false;
public static boolean estimateGapProb = false;
public static boolean estimateDelta = false;
public static boolean estimateEpsilon = false;
public static boolean exitInError = true;
public static boolean estimateParameters = false;
public static int bandWidth = 101; // diagonal alignment band width
public static int offset = 15;
static String fileExt = new String("paa"); // PA-file extension
static String version = "0.5 alpha 0";
public static String protModel = "wag";
static int paFontSize = 11;
static String paFontName = "sansserif";
static String clustalwPath;
static String folderPath;
static String tempFolder;
static int wWidth = 800; // window size
static int wHeight = 300;
static OutFile log;
public SubstitutionModel sm;
AlignmentNode root;
ResultWindow rw;
public ProAlign() {
// System.out.println("ProAlign");
}
public ProAlign(String[] args){
defBandWidth = bandWidth;
defOffset = offset;
startNewLog("proalign.log");
setUserData();
if(args.length>0) {
ReadArguments ra = new ReadArguments(ProAlign.this, args);
}
sm = new SubstitutionModel(ProAlign.this);
if(ProAlign.isDna){
sm.jcDnaModel();
} else {
if(ProAlign.protModel.equals("dayhoff")) {
sm.dayhoffProteinModel();
} else if(ProAlign.protModel.equals("jtt")) {
sm.jttProteinModel();
} else {
sm.wagProteinModel();
}
}
if(nogui) {
try {
RunCommandLine rcl = new RunCommandLine(ProAlign.this);
} catch(Exception e) { }
} else {
rw = new ResultWindow(ProAlign.this);
rw.setSize(wWidth,wHeight);
isResultWindow = true;
rw.setVisible(true);
}
}
/**
* Keeps count on the new nodes that are created. Gives a unique number.
*/
int getNodeNumber() {
nodeNumber++;
return nodeNumber;
}
/**
* Resets the counter.
*/
void setNodeNumber(int i) {
nodeNumber = i;
}
/**
* Keep log.
*/
public void startNewLog(String file) {
try {
log = new OutFile(file);
} catch(Exception e) { }
String date = Calendar.getInstance().getTime().toString();
log.println("\n------------------------------------");
log.println("ProAlign - starting a new event log.");
log.println(" "+date);
log.println("------------------------------------\n");
log.flush();
}
/**
* Get userdata from file
*/
void setUserData() {
UserSettings user = new UserSettings();
String[] userdata = user.readSettings();
try {
if(new File(userdata[0]).isDirectory())
folderPath = new File(userdata[0]).getAbsolutePath();
} catch (Exception e) {
folderPath = new String(".");
}
try {
if(new File(userdata[1]).isFile())
clustalwPath = new File(userdata[1]).getAbsolutePath();
} catch (Exception e) {
clustalwPath = new String("clustalw");
}
try {
if(new File(userdata[2]).isDirectory())
folderPath = new File(userdata[0]).getAbsolutePath();
} catch (Exception e) {
if(System.getProperty("os.name").startsWith("Windows")){
tempFolder = "C:\\TEMP";
} else {
tempFolder = "/tmp";
}
}
}
static void log(String txt) {
if(DEBUG) {
log.println(txt);
log.flush();
}
}
/**
* Main class. Takes command line arguments to run with scripts.
*/
public static void main(String[] args) {
try {
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception e) { }
ProAlign pa = new ProAlign(args);
}
}
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