+++ /dev/null
-/***************************************************************
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
-*
-* @author: Copyright (C) Tim Carver
-*
-***************************************************************/
-
-package ext.jemboss;
-
-import java.util.*;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.net.InetAddress;
-
-
-/**
-*
-* Contains all property information about the client
-* and the server.
-*
-*/
-public class JembossParams
-{
-
-/** denotes a server is OK */
- static public final int SERVER_OK = 0;
-/** denotes a server is giving errors */
- static public final int SERVER_ERR = 1;
-/** denotes a server is not responding */
- static public final int SERVER_DOWN = 2;
-
- // these are the things that could be set
- private boolean useHTTPSProxy = false;
- private String useHTTPSProxyName = "useHTTPSProxy";
-
- private boolean useProxy = false;
- private String useProxyName = "proxy.use";
-
- private String proxyHost = "wwwcache";
- private String proxyHostName = "proxy.host";
-
- private int proxyPortNum = 8080;
- private String proxyPortNumName = "proxy.port";
-
-//browser proxy
-
- /** use a separate proxy for browsing the web */
- private boolean useBrowserProxy = false;
- /** property name for using separate proxy for browsing the web */
- private String useBrowserProxyName = "browserProxy.use";
- /** browser proxy host */
- private String browserProxyHost = "wwwcache";
- /** property name for browser proxy host */
- private String browserProxyHostName = "browserProxy.host";
- /** browser proxy port */
- private int browserProxyPort = 8080;
- /** property name for browser proxy port */
- private String browserProxyPortName = "browserProxy.port";
-
- private boolean useTFM;
- private String useTFMName = "tfm.use";
-
- /** use proxy authentication */
- private boolean useProxyAuth = false;
- /** property name for using proxy authentication */
- private String useProxyAuthName = "proxy.auth";
-
- private String proxyAuthUser = "";
- private String proxyAuthUserName = "proxy.user";
-
- private String proxyAuthPasswd = "";
- private String proxyAuthPasswdName = "proxy.passwd";
-
- private boolean proxyOverride = false;
- private String proxyOverrideName = "proxy.override";
-
- /** use unix authentication to run applications on the server */
- private boolean useAuth = false;
- /** property name for using unix authentication */
- private String useAuthName = "user.auth";
-
- /** public services URL */
- private String publicSoapURL =
- "http://anaplog.compbio.dundee.ac.uk:8080/axis/services";
- /** property name for public services URL */
- private String publicSoapURLName = "server.public";
-
- /** private services URL */
- private String privateSoapURL =
- "http://anaplog.compbio.dundee.ac.uk:8080/axis/services";
- /** property name for private services URL */
- private String privateSoapURLName = "server.private";
-
- /** service name */
- private String soapService = "JembossServer";
- /** property name for service name */
- private String soapServiceName = "VAMSAS Services";
-
- /** private service name */
- private String privateSoapService = "JembossServer";
- /** property name for private service name */
- private String privateSoapServiceName = "VAMSAS Services";
-
- /** public service name */
- private String publicSoapService = "JembossServer";
- /** property name for public service name */
- private String publicSoapServiceName = "VAMSAS Services";
-
- //soap options
- private boolean debug = false;
- private String debugName = "jemboss.debug";
-
- /** batch mode support */
- private boolean hasBatchMode = true;
- /** property name for batch mode support */
- private String hasBatchModeName = "jemboss.hasbatchmode";
- /** interactive mode support */
- private boolean hasInteractiveMode = true;
- /** property name for interactive mode support */
- private String hasInteractiveModeName = "jemboss.hasinteractivemode";
- /** current mode for running an application */
- private String currentMode = "interactive";
- /** property name for current mode */
- private String currentModeName = "jemboss.mode";
-
- // server lists for redundancy
- private String serverPublicList = "";
- private String serverPublicListName = "server.publiclist";
-
- private String serverPrivateList = "";
- private String serverPrivateListName = "server.privatelist";
-
- // we don't remember these perhaps we should for captive systems
- private String serviceUserName = "jalview";
- private String serviceUserNameName = "user.name";
- private char[] servicePasswd = null;
- /** services password */
- private byte[] servicePasswdByte = null;
-
- Properties jembossSettings;
-
- // Internal flags to help in the dynamic evaluation of properties
- private boolean useJavaProxy = false;
- private String javaProxyPort = "";
- private String javaProxyHost = "";
- private boolean useJavaNoProxy = false;
- private String javaNoProxy = "";
- private Vector javaNoProxyEntries;
- private int javaProxyPortNum = 8080;
-
- // structures for server redundancy
- private boolean publicServerFailOver = false;
- private boolean privateServerFailOver = false;
- private Hashtable serverStatusHash;
- private Vector publicServers;
- private Vector privateServers;
-
- /** Jemboss java server */
- private static boolean jembossServer = false;
- /** property name for Jemboss java server */
- private String jembossServerName = "jemboss.server";
-
- /** cygwin */
- private static String cygwin = null;
- /** property name for Jemboss java server */
- private String cygwinName = "cygwin";
-
- //EMBOSS directories
- /** plplot library location */
- private String plplot = "/usr/local/share/EMBOSS/";
- /** property name for plplot library location */
- private String plplotName = "plplot";
- /** emboss data location */
- private String embossData = "/usr/local/share/EMBOSS/data/";
- /** property name for emboss data location */
- private String embossDataName = "embossData";
- /** emboss binary location */
- private String embossBin = "/usr/local/bin/";
- /** property name for emboss binary location */
- private String embossBinName = "embossBin";
- /** emboss path environment variable */
- private String embossPath = "/usr/bin/:/bin";
- /** property name for emboss path environment variable */
- private String embossPathName = "embossPath";
- /** emboss environment */
- private String embossEnvironment = "";
- /** property name for emboss environment */
- private String embossEnvironmentName = "embossEnvironment";
- /** acd file location */
- private String acdDirToParse = "/usr/local/share/EMBOSS/acd/";
- /** property name for acd file location */
- private String acdDirToParseName = "acdDirToParse";
-
- //EMBOSS Application pages
- /** documentation URL */
- private String embURL = "http://www.uk.embnet.org/Software/EMBOSS/Apps/";
- /** property name for documentation URL */
- private String embossURL = "embossURL";
-
- // user properties
- /** user home directory */
- private String userHome = System.getProperty("user.home");
- /** property name for user home directory */
- private String userHomeName = "user.home";
-
-
-/**
-*
-* Loads and holds the properties
-*
-*/
- public JembossParams()
- {
- Properties defaults = new Properties();
- ClassLoader cl = this.getClass().getClassLoader();
-
- // initialize data structures
- serverStatusHash = new Hashtable();
- publicServers = new Vector();
- privateServers = new Vector();
-
- // initialize settings from table above
- defaults.put(userHomeName,userHome);
- defaults.put(embossURL,embURL);
- defaults.put(plplotName,plplot);
- defaults.put(embossDataName,embossData);
- defaults.put(embossBinName,embossBin);
- defaults.put(embossPathName,embossPath);
- defaults.put(embossEnvironmentName,embossEnvironment);
- defaults.put(acdDirToParseName,acdDirToParse);
-
- defaults.put(useBrowserProxyName, new Boolean(useBrowserProxy).toString());
- defaults.put(browserProxyHostName,browserProxyHost);
- defaults.put(browserProxyPortName,new Integer(browserProxyPort).toString());
-
- defaults.put(useTFMName,new Boolean(useTFM).toString());
-
- defaults.put(useProxyName, new Boolean(useProxy).toString());
- defaults.put(useHTTPSProxyName, new Boolean(useHTTPSProxy).toString());
- defaults.put(proxyHostName,proxyHost);
- defaults.put(proxyPortNumName, new Integer(proxyPortNum).toString());
- defaults.put(useProxyAuthName, new Boolean(useProxyAuth).toString());
- defaults.put(proxyAuthUserName, proxyAuthUser);
- defaults.put(proxyAuthPasswdName, proxyAuthPasswd);
- defaults.put(proxyOverrideName, new Boolean(proxyOverride).toString());
- defaults.put(useAuthName, new Boolean(useAuth).toString());
- defaults.put(publicSoapURLName, publicSoapURL);
- defaults.put(privateSoapURLName, privateSoapURL);
- defaults.put(privateSoapServiceName, privateSoapService);
- defaults.put(publicSoapServiceName, publicSoapService);
- defaults.put(debugName, new Boolean(debug).toString());
- defaults.put(hasBatchModeName, new Boolean(hasBatchMode).toString());
- defaults.put(hasInteractiveModeName, new Boolean(hasInteractiveMode).toString());
- defaults.put(currentModeName, currentMode);
- defaults.put(serverPublicListName, serverPublicList);
- defaults.put(serverPrivateListName, serverPrivateList);
- defaults.put(serviceUserNameName, serviceUserName);
-
- // load into real settings
- jembossSettings = new Properties(defaults);
-
- // try out of the classpath
- try
- {
- jembossSettings.load(cl.getResourceAsStream("resources/jemboss.properties"));
- }
- catch (Exception e)
- {
- if(debug)
- System.out.println("Didn't find properties file in classpath.");
- }
-
- // override with local system settings
- loadIn(System.getProperty("user.dir"));
-
- // override with local user settings
- loadIn(System.getProperty("user.home"));
-
- // update our settings
- updateSettingsFromProperties();
-
- if(System.getProperty("useHTTPSProxy") != null)
- if(System.getProperty("useHTTPSProxy").equalsIgnoreCase("true"))
- useHTTPSProxy=true;
-
- // set up for overrides
- javaNoProxyEntries = new Vector();
- if(System.getProperty("proxyPort") != null)
- {
- if(System.getProperty("proxyHost") != null)
- {
- useJavaProxy = true;
- useProxy = useJavaProxy;
- useBrowserProxy = useJavaProxy;
-
- javaProxyPort = System.getProperty("proxyPort");
- javaProxyPortNum = Integer.parseInt(javaProxyPort);
- javaProxyHost = System.getProperty("proxyHost");
-
- browserProxyHost = javaProxyHost;
- browserProxyPort = javaProxyPortNum;
-
- if(System.getProperty("http.nonProxyHosts") != null)
- {
- useJavaNoProxy = true;
- javaNoProxy = System.getProperty("http.nonProxyHosts");
- StringTokenizer tok = new StringTokenizer(javaNoProxy,"|");
- while (tok.hasMoreTokens())
- {
- String toks = tok.nextToken() + "/";
- javaNoProxyEntries.add(toks);
- }
- }
- }
- }
-
- }
-
- /**
- *
- * Load a property from the jemboss.property file.
- * @param folder location of jemboss.property
- *
- */
- private void loadIn(String folder)
- {
- FileInputStream in = null;
- try
- {
- String fs = System.getProperty("file.separator");
- in = new FileInputStream(folder + fs + "jemboss.properties");
- jembossSettings.load(in);
- }
- catch (java.io.FileNotFoundException e)
- {
- in = null;
- if(debug)
- System.out.println("Can't find properties file in"+folder+"."+
- " Using defaults.");
- }
- catch (java.io.IOException e)
- {
- if(debug)
- System.out.println("Can't read properties file. " +
- "Using defaults.");
- }
- finally
- {
- if (in != null)
- {
- try { in.close(); } catch (java.io.IOException e) { }
- in = null;
- }
- }
-
- }
-
- /**
- *
- * Update the property settings for jembossSettings.
- *
- */
- protected void updateSettingsFromProperties()
- {
-
- try
- {
- String tmp;
-
- userHome = jembossSettings.getProperty(userHomeName);
- embURL = jembossSettings.getProperty(embossURL);
- plplot = jembossSettings.getProperty(plplotName);
- embossData = jembossSettings.getProperty(embossDataName);
- embossBin = jembossSettings.getProperty(embossBinName);
- embossPath = jembossSettings.getProperty(embossPathName);
- embossEnvironment = jembossSettings.getProperty(embossEnvironmentName);
- acdDirToParse = jembossSettings.getProperty(acdDirToParseName);
- tmp = jembossSettings.getProperty(jembossServerName);
- jembossServer = new Boolean(tmp).booleanValue();
-
- cygwin = jembossSettings.getProperty(cygwinName);
-
- tmp = jembossSettings.getProperty(useHTTPSProxyName);
- useHTTPSProxy = new Boolean(tmp).booleanValue();
- tmp = jembossSettings.getProperty(useProxyName);
- useProxy = new Boolean(tmp).booleanValue();
- proxyHost = jembossSettings.getProperty(proxyHostName);
- tmp = jembossSettings.getProperty(proxyPortNumName);
- proxyPortNum = Integer.parseInt(tmp);
-
- tmp = jembossSettings.getProperty(useBrowserProxyName);
- useBrowserProxy = new Boolean(tmp).booleanValue();
- browserProxyHost = jembossSettings.getProperty(browserProxyHostName);
- tmp = jembossSettings.getProperty(browserProxyPortName);
- browserProxyPort = Integer.parseInt(tmp);
-
- tmp = jembossSettings.getProperty(useTFMName);
- useTFM = new Boolean(tmp).booleanValue();
-
- tmp = jembossSettings.getProperty(useProxyAuthName);
- useProxyAuth = new Boolean(tmp).booleanValue();
- proxyAuthUser = jembossSettings.getProperty(proxyAuthUserName);
- proxyAuthPasswd = jembossSettings.getProperty(proxyAuthPasswdName);
- tmp = jembossSettings.getProperty(proxyOverrideName);
- proxyOverride = new Boolean(tmp).booleanValue();
- tmp = jembossSettings.getProperty(useAuthName);
- useAuth = new Boolean(tmp).booleanValue();
- publicSoapURL = jembossSettings.getProperty(publicSoapURLName);
- privateSoapURL = jembossSettings.getProperty(privateSoapURLName);
- soapService = jembossSettings.getProperty(soapServiceName);
- privateSoapService = jembossSettings.getProperty(privateSoapServiceName);
- publicSoapService = jembossSettings.getProperty(publicSoapServiceName);
- tmp = jembossSettings.getProperty(debugName);
- debug = new Boolean(tmp).booleanValue();
- tmp = jembossSettings.getProperty(hasBatchModeName);
- hasBatchMode = new Boolean(tmp).booleanValue();
- tmp = jembossSettings.getProperty(hasInteractiveModeName);
- hasInteractiveMode = new Boolean(tmp).booleanValue();
- currentMode = jembossSettings.getProperty(currentModeName);
- serverPublicList = jembossSettings.getProperty(serverPublicListName);
- serverPrivateList = jembossSettings.getProperty(serverPrivateListName);
-// serviceUserName = jembossSettings.getProperty(serviceUserNameName);
- }
- catch (Exception e) { }
- }
-
-/**
-*
-* Initialize the server redundancy data. This is a separate
-* method because the server info might not be initialized in
-* the constructor, but may be imported later from the command line.
-*
-*/
- protected void setupServerRedundancy()
- {
- if (!serverPublicList.equals(""))
- {
- if(debug)
- System.out.println("JembossParams: Redundant public servers\n "
- +serverPublicList);
-
- publicServerFailOver = true;
- StringTokenizer tok = new StringTokenizer(serverPublicList,"|");
- while (tok.hasMoreTokens())
- {
- String toks = tok.nextToken();
- publicServers.add(toks);
- if(debug)
- System.out.println(" Entry " + toks);
-
- serverStatusHash.put(toks, new Integer(SERVER_OK));
- }
- }
-
- if(!serverPrivateList.equals(""))
- {
- if(debug)
- System.out.println("JembossParams: Redundant private servers\n "
- +serverPrivateList);
-
- privateServerFailOver = true;
- StringTokenizer tok = new StringTokenizer(serverPrivateList,"|");
- while (tok.hasMoreTokens())
- {
- String toks = tok.nextToken();
- privateServers.add(toks);
- if(debug)
- System.out.println(" Entry " + toks);
-
- serverStatusHash.put(toks,new Integer(SERVER_OK));
- }
- }
- }
-
-
-/**
-*
-* If using a proxy server
-*
-*/
- public boolean getUseProxy()
- {
- return useProxy;
- }
-
-
-/**
-*
-* If using an https proxy server
-*
-*/
- public boolean getUseHTTPSProxy()
- {
- return useHTTPSProxy;
- }
-
-
-/**
-*
-* If using a proxy server for a given URL
-* @param s the URL we wish to connect to
-*
-*/
- public boolean getUseProxy(String s)
- {
- if(proxyOverride)
- return useProxy;
- else
- {
- if(!useJavaProxy)
- return useProxy;
- else
- {
- boolean jp = true;
- if (useJavaNoProxy)
- {
- int ip = javaNoProxyEntries.size();
- for(int j = 0 ; j<ip ; ++j)
- if(s.indexOf((String)javaNoProxyEntries.get(j).toString()) != -1)
- jp = false;
- }
- return jp;
- }
- }
- }
-
-/**
-*
-* The name of the proxy server
-* @return name of the proxy host
-*
-*/
- public String getProxyHost()
- {
- if (proxyOverride)
- return proxyHost;
- else
- {
- if(!useJavaProxy)
- return proxyHost;
- else
- return javaProxyHost;
- }
- }
-
-/**
-*
-* The port the proxy server listens on
-* @return proxy port number
-*
-*/
- public int getProxyPortNum()
- {
- if(proxyOverride)
- return proxyPortNum;
- else
- {
- if(!useJavaProxy)
- return proxyPortNum;
- else
- return javaProxyPortNum;
- }
- }
-
-/**
-*
-* Determine if the a proxy server is being used for web browsing
-* @return true if using a proxy server for the browser
-*
-*/
- public boolean isBrowserProxy()
- {
- return useBrowserProxy;
- }
-
-/**
-*
-* Get the name of the proxy server for the browser
-* @return the name of the proxy host
-*
-*/
- public String getBrowserProxyHost()
- {
- return browserProxyHost;
- }
-
-
-/**
-*
-* The port number of the proxy server for the browser
-* @return proxy port number
-*
-*/
- public int getBrowserProxyPort()
- {
- return browserProxyPort;
- }
-
-
- public boolean isUseTFM() { return useTFM; }
-
-
-/**
-*
-* If using authenticate with the proxy
-* @return true if unix authentication used
-*
-*/
- public boolean getUseProxyAuth()
- {
- return useProxyAuth;
- }
-
-/**
-*
-* Username needed to use for the proxy server
-*
-*/
- public String getProxyAuthUser()
- {
- return proxyAuthUser;
- }
-
-/**
-*
-* Password needed to use for the proxy server
-*
-*/
- public String getProxyAuthPasswd()
- {
- return proxyAuthPasswd;
- }
-
-/**
-*
-* A description of the proxy settings
-* @return a description of the proxy settings
-*
-*/
- public String proxyDescription()
- {
- String pdesc = "";
- if (proxyOverride)
- {
- if(useProxy)
- {
- String spnum = new Integer(proxyPortNum).toString();
- pdesc = "Current Settings: " + "Proxy Host: " + proxyHost +
- " Proxy Port: " + spnum;
- }
- else
- pdesc = "No proxies, connecting direct.";
- }
- else
- {
- if (useJavaProxy)
- {
- pdesc = "Settings Imported from Java: " + "Proxy Host: " + javaProxyHost
- + " Proxy Port: " + javaProxyPort;
- if(useJavaNoProxy)
- pdesc = pdesc + "\nNo Proxy On: " + javaNoProxy;
- }
- else
- {
- if(useProxy)
- {
- String spnum = new Integer(proxyPortNum).toString();
- pdesc = "Current Settings: " + "Proxy Host: " + proxyHost +
- " Proxy Port: " + spnum;
- }
- else
- pdesc = "No proxies, connecting direct.";
- }
- }
- return pdesc;
- }
-
-/**
-*
-* Whether the main service requires authentication
-* @return true if the server is using unix authentication
-*
-*/
- public boolean getUseAuth()
- {
- return useAuth;
- }
-
-/**
-*
-* Returns the URL of the public soap server
-* @return the public services URL
-*
-*/
- public String getPublicSoapURL()
- {
- return publicSoapURL;
- }
-
-/**
-*
-* @return true if using a Jemboss server
-*
-*/
- public static boolean isJembossServer()
- {
- return jembossServer;
- }
-
-/**
-*
-* @return true if using cygwin
-*
-*/
- public static boolean isCygwin()
- {
- if(cygwin == null || cygwin.equals(""))
- return false;
- else
- return true;
- }
-
-
-/**
-*
-* Get the cygwin root
-* @return cygwin root
-*
-*/
- public String getCygwinRoot()
- {
- return cygwin;
- }
-
-
-
-/**
-*
-* Get the location of plplot
-* @return the location of plplot
-*
-*/
- public String getPlplot()
- {
- return plplot;
- }
-
-/**
-*
-* Get the user home directory
-* @return the user home directory
-*
-*/
- public String getUserHome()
- {
- return userHome;
- }
-
-/**
-*
-* Set the user home directory property
-* @param s the user home directory
-*
-*/
- public void setUserHome(String s)
- {
- userHome = s;
- }
-
-/**
-*
-* @return the documentation URL
-*
-*/
- public String getembURL()
- {
- return embURL;
- }
-
-/**
-*
-* @return the location of the emboss data
-*
-*/
- public String getEmbossData()
- {
- return embossData;
- }
-
-/**
-*
-* @return the location of the emboss binaries
-*
-*/
- public String getEmbossBin()
- {
- return embossBin;
- }
-
-/**
-*
-* Get the path for emboss
-* @return the path for emboss
-*
-*/
- public String getEmbossPath()
- {
- return embossPath;
- }
-
-/**
-*
-* Get the environment for emboss
-* @return the environment for emboss
-*
-*/
- public String getEmbossEnvironment()
- {
- embossEnvironment = embossEnvironment.trim();
- embossEnvironment = embossEnvironment.replace(':',' ');
- embossEnvironment = embossEnvironment.replace(',',' ');
- return embossEnvironment;
- }
-
-/**
-*
-* Get the emboss environment as a String array
-* @return the emboss environment as a String array
-*
-*/
- public String[] getEmbossEnvironmentArray(String[] envp)
- {
- embossEnvironment = embossEnvironment.trim();
- embossEnvironment = embossEnvironment.replace(':',' ');
- embossEnvironment = embossEnvironment.replace(',',' ');
-
- if(embossEnvironment.equals(""))
- return envp;
-
- StringTokenizer st = new StringTokenizer(embossEnvironment," ");
- int n=0;
- while(st.hasMoreTokens())
- {
- st.nextToken();
- n++;
- }
-
- int sizeEnvp = envp.length;
- String environ[] = new String[n+sizeEnvp];
- st = new StringTokenizer(embossEnvironment," ");
- for(int i=0;i<sizeEnvp;i++)
- environ[i] = envp[i];
-
- n=sizeEnvp;
- while(st.hasMoreTokens())
- {
- environ[n] = new String(st.nextToken());
- n++;
- }
-
- return environ;
- }
-
-/**
-*
-* Acd file location
-* @return acd file location
-*
-*/
- public String getAcdDirToParse()
- {
- return acdDirToParse;
- }
-
-/**
-*
-* Set the URL of the public soap server
-* @param s URL of the public services
-*
-*/
- public void setPublicSoapURL(String s)
- {
- publicSoapURL = s;
- }
-
-/**
-*
-* Returns the URL of the private soap server
-* @return URL of the private services
-*
-*/
- public String getPrivateSoapURL()
- {
- return privateSoapURL;
- }
-
-/**
-*
-* Set the URL of the private soap server
-* @param s URL of the private services
-*
-*/
- public void setPrivateSoapURL(String s)
- {
- privateSoapURL = s;
- }
-
-/**
-*
-* Return whether we have failover on the public server
-*
-*/
- public boolean getPublicServerFailover()
- {
- return publicServerFailOver;
- }
-
-/**
-*
-* Return whether we have failover on the private server
-*
-*/
- public boolean getPrivateServerFailover()
- {
- return privateServerFailOver;
- }
-
-/**
-*
-* Return a vector containing the list of public servers
-*
-*/
- public Vector getPublicServers()
- {
- return publicServers;
- }
-
-/**
-*
-* Return a vector containing the list of private servers
-*
-*/
- public Vector getPrivateServers()
- {
- return privateServers;
- }
-
-/**
-*
-* Mark a server as bad
-*
-*/
- public void setServerStatus(String server, int i)
- {
- serverStatusHash.put(server, new Integer(i));
- }
-
-/**
-*
-* Return the username needed for the remote service
-* @return the username
-*
-*/
- public String getServiceUserName()
- {
- return serviceUserName;
- }
-
-/**
-*
-* Save the username needed for the remote service
-* @param newUserName the username
-*
-*/
- public void setServiceUserName(String newUserName)
- {
- serviceUserName = newUserName;
- }
-
-/**
-*
-* Return the password needed for the remote service
-* @return password
-*
-*/
- public char[] getServicePasswd()
- {
- return servicePasswd;
- }
-
-/**
-*
-* Return the password needed for the remote service
-* @return password
-*
-*/
- public byte[] getServicePasswdByte()
- {
- return servicePasswdByte;
- }
-
-/**
-*
-* Return the password as byte array
-*
-*/
- private static byte[] toByteArr(char ch[])
- {
- int len = ch.length;
- byte msb[] = new byte[len];
-
- for(int i=0;i<len;i++)
- msb[i] = (byte)(ch[i]);
- return msb;
- }
-
-
-/**
-*
-* Save the password needed for the remote service
-* @param newPasswd the username
-*
-*/
- public void setServicePasswd(char[] newPasswd)
- {
- int csize = newPasswd.length;
- servicePasswd = new char[csize];
-
- for(int i=0;i<csize;i++)
- servicePasswd[i] = newPasswd[i];
-
- servicePasswdByte = toByteArr(newPasswd);
- }
-
-/**
-*
-* Get the name of the soap service
-* @return soap service name
-*
-*/
- public String getSoapService()
- {
- return soapService;
- }
-
-/**
-*
-* Get the name of the private soap service
-* @return private service name
-*
-*/
- public String getPrivateSoapService()
- {
- return privateSoapService;
- }
-
-/**
-*
-* Set the name of the private soap service
-* @param s private service name
-*
-*/
- public void setPrivateSoapService(String s)
- {
- privateSoapService = s;
- }
-
-/**
-*
-* Get the name of the public soap service we're using
-* @return public service name
-*
-*/
- public String getPublicSoapService()
- {
- return publicSoapService;
- }
-
-/**
-*
-* Set the name of the public soap service we're using
-* @param s public service name
-*
-*/
- public void setPublicSoapService(String s)
- {
- publicSoapService = s;
- }
-
-/**
-*
-* A description of the server settings
-* @return description of the services
-*
-*/
- public String serverDescription()
- {
- String serverdesc = "Current Settings:"
- +"\nPublic Server: "+publicSoapURL
- +"\nPrivate Server: "+privateSoapURL
- +"\nPublic SOAP service: "+publicSoapService
- +"\nPrivate SOAP service: "+privateSoapService;
- return serverdesc;
- }
-
-/**
-*
-* Whether to show debugging information
-*
-*/
- public boolean getDebug()
- {
- return debug;
- }
-
-/**
-*
-* Whether this service supports batch mode
-* @return true if batch mode supported
-*
-*/
- public boolean getHasBatchMode()
- {
- return hasBatchMode;
- }
-
-/**
-*
-* Whether this service supports interactive mode
-* @return true if interactive mode supported
-*
-*/
- public boolean getHasInteractiveMode()
- {
- return hasInteractiveMode;
- }
-
-/**
-*
-* The current mode (interactive or batch).
-* @return a String containing the current mode
-*
-*/
- public String getCurrentMode()
- {
- if(hasInteractiveMode)
- {
- if (hasBatchMode)
- return currentMode;
- else
- return "interactive";
- }
- else
- {
- if (hasBatchMode)
- return "batch";
- else
- return currentMode;
- }
- }
-
-/**
-*
-* Set the current mode (interactive or batch).
-* @param newMode The new execution mode
-*
-*/
- public void setCurrentMode(String newMode)
- {
- currentMode = newMode;
- }
-
-/**
-*
-* Return the mode list as a vector, suitable for loading into
-* a combobox.
-* @return mode list
-*
-*/
- public Vector modeVector()
- {
- Vector mv = new Vector();
- if (hasInteractiveMode)
- {
- if (hasBatchMode)
- {
- if (currentMode.equals("interactive"))
- {
- mv.add("interactive");
- mv.add("batch");
- }
- else if (currentMode.equals("batch"))
- {
- mv.add("batch");
- mv.add("interactive");
- }
- else
- {
- mv.add(currentMode);
- mv.add("interactive");
- mv.add("batch");
- }
- }
- else
- mv.add("interactive");
- }
- else
- {
- if(hasBatchMode)
- mv.add("batch");
- }
- return mv;
- }
-
-/**
-*
-* Update the properties structure.
-* This doesn't update the actual properties, just the Properties object
-* so you must call updateSettingsFromProperties yoursefl
-*
-* @param name A String naming the property to be updated
-* @param newvalue A String containing the new value of the property
-*
-*/
- public void updateJembossProperty(String name, String newvalue)
- {
- if (jembossSettings.getProperty(name) != null)
- jembossSettings.setProperty(name,newvalue);
- }
-
-/**
-*
-* Parse a key=value string to update the properties structure
-* @param entry String containing a key=value message
-*
-*/
- public void updateJembossPropString(String entry)
- {
- int isep = entry.indexOf('=');
- if(isep != -1)
- {
- String pkey = entry.substring(0,isep);
- String pvalue = entry.substring(isep+1);
- updateJembossProperty(pkey, pvalue);
- }
- }
-
-/**
-*
-* Parse an array of key=value strings to update the properties structure
-* @param entries Array of Strings containing key=value messages
-*
-*/
- public void updateJembossPropStrings(String[] entries)
- {
- for (int i=0; i < entries.length; ++i)
- updateJembossPropString(entries[i]);
-
- updateSettingsFromProperties();
- setupServerRedundancy();
- }
-
-/**
-*
-* Update properties from a Hashtable
-* @param hash Hashtable containg properties
-*
-*/
- public void updateJembossPropHash(Hashtable hash)
- {
- Enumeration enumer = hash.keys();
- while(enumer.hasMoreElements())
- {
- String thiskey = (String)enumer.nextElement().toString();
- String thisval = (String)hash.get(thiskey);
- updateJembossProperty(thiskey,thisval);
- }
- updateSettingsFromProperties();
- }
-
-}
-
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-\r
-\r
-package jalview.gui;\r
-\r
-import jalview.jbgui.GAlignFrame;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\r
-import jalview.ws.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.print.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.datatransfer.*;\r
-\r
-\r
-public class AlignFrame extends GAlignFrame\r
-{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- public String currentFileFormat = "Jalview";\r
-\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
-\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
-\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
-\r
- addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameActivated(InternalFrameEvent evt)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- { alignPanel.requestFocus(); }\r
- });\r
-\r
- }\r
- });\r
-\r
- }\r
-\r
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
- , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},\r
- currentFileFormat);\r
-\r
- chooser.setAcceptAllFileFilterUsed(false);\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- currentFileFormat = chooser.getSelectedFormat();\r
-\r
- if (currentFileFormat.equals("Jalview"))\r
- {\r
- String shortName = title.replace('/', '_');\r
- title = title.replace('\\', '_');\r
- String choice = chooser.getSelectedFile().getPath();\r
- Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,\r
- choice);\r
- // USE Jalview2XML to save this file\r
- return;\r
- }\r
-\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
- out.println(output);\r
- out.close();\r
- }\r
- catch(Exception ex){}\r
- }\r
-\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
- htmlOutput = null;\r
- }\r
-\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makePNG();\r
- }\r
-\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makeEPS();\r
- }\r
-\r
-\r
- public void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- //Putting in a thread avoids Swing painting problems\r
- PrintThread thread = new PrintThread();\r
- thread.start();\r
- }\r
-\r
- class PrintThread extends Thread\r
- {\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
- printJob.setPrintable(alignPanel, pf);\r
- if (printJob.printDialog())\r
- {\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
-\r
-\r
-\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- this.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
-\r
- void updateEditMenuBar()\r
- {\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])historyList.get(0);\r
- undoMenuItem.setText("Undo "+history[0]);\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setText("Undo");\r
- }\r
-\r
- if(redoList.size()>0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])redoList.get(0);\r
- redoMenuItem.setText("Redo "+history[0]);\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setText("Redo");\r
- }\r
- }\r
-\r
- public void addHistoryItem(String type)\r
- {\r
- // must make sure we add new sequence objects her, not refs to the existing sequences\r
- redoList.clear();\r
-\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).getSequence());\r
- }\r
-\r
-\r
- historyList.add(0, new Object[]{type, seq} );\r
- updateEditMenuBar();\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])historyList.remove(0);\r
- // add the redo state before continuing!!\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).\r
- getSequence());\r
- }\r
- /////////\r
-\r
- redoList.add(0, new Object[] {history[0], seq});\r
-\r
- seq = (SequenceI[]) history[1];\r
- AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment( new Alignment(seq) );\r
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
- updateEditMenuBar();\r
- for(int i=0; i<old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (sg == null)\r
- return;\r
-\r
- if (up)\r
- {\r
- for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
- continue;\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
- continue;\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
- continue;\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
- continue;\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
- }\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- StringBuffer buffer= new StringBuffer();\r
-\r
- Hashtable orderedSeqs = new Hashtable();\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
- }\r
-\r
- int index=0;\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = null;\r
- while( seq == null )\r
- {\r
- if(orderedSeqs.containsKey(index+""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
- }\r
- else\r
- index++;\r
- }\r
-\r
- buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
- }\r
- c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
-\r
- }\r
-\r
-\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
- paste(true);\r
- }\r
-\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("Paste");\r
- paste(false);\r
- }\r
-\r
- void paste(boolean newAlignment)\r
- {\r
- try{\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
- if (contents == null)\r
- return;\r
-\r
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
-\r
- if(!newAlignment)\r
- viewport.alignment.addSequence(sequence);\r
- else\r
- seqs.add(sequence);\r
- }\r
-\r
- if(newAlignment)\r
- {\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- seqs.toArray(newSeqs);\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
- String newtitle = new String("Copied sequences");\r
- if( title.startsWith("Copied sequences"))\r
- newtitle = title;\r
- else\r
- newtitle = newtitle.concat("- from "+title);\r
-\r
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- }\r
- else\r
- {\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- }catch(Exception ex){}// could be anything being pasted in here\r
-\r
- }\r
-\r
-\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
- }\r
-\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("Delete");\r
- if (viewport.getSelectionGroup() == null)\r
- return;\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
-\r
- if(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\r
- else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setClosed(true);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
-\r
- }\r
-\r
-\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])redoList.remove(0);\r
- SequenceI[] seq = (SequenceI[]) history[1];\r
- viewport.setAlignment( new Alignment(seq) );\r
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
- sg.setEndRes(viewport.alignment.getWidth());\r
- viewport.setSelectionGroup(sg);\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
-\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0,min);\r
-\r
- if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
- }\r
-\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
- if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
- if(!sg.adjustForRemoveRight(max))\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
-\r
-\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete gapped columns");\r
- viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete all gaps");\r
- SequenceI current;\r
- int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
- jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
- }\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340,110);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
-\r
- }\r
-\r
-\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- FontChooser fc = new FontChooser( alignPanel );\r
- }\r
-\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowFullId( fullSeqId.isSelected() );\r
-\r
- alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
- scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
- scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
- scaleRight.setVisible( wrapMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText( viewTextMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
- {\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
- }\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
- return;\r
- }\r
- viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- return;\r
-\r
- JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- };\r
- });\r
-\r
- alignPanel.setOverviewPanel( overview );\r
-\r
-\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( null );\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- abovePIDThreshold.setSelected(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new HydrophobicColourScheme() );\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme() );\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme() );\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
- }\r
-\r
-\r
-\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if ( viewport.getAbovePIDThreshold() )\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
-\r
-\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\r
-\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
-\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- ccs = new ConservationColourScheme(c, cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
- viewport.setGlobalColourScheme(ccs);\r
-\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
-\r
- }\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
-\r
-\r
- if(viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
- }\r
- else if(cs!=null)\r
- {\r
- try{\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
- }\r
-\r
- if( viewport.getConservationSelected() )\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = ccs;\r
- }\r
- else if(cs!=null)\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- }\r
-\r
- }\r
- }\r
-\r
- if(alignPanel.getOverviewPanel()!=null)\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
- }\r
-\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getConservationSelected())\r
- {\r
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
- "Background");\r
- SliderPanel.showConservationSlider();\r
- }\r
- }\r
-\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
-\r
- modifyConservation_actionPerformed(null);\r
- }\r
-\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
-\r
- conservationMenuItem.setSelected(false);\r
- viewport.setConservationSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
-\r
- modifyPID_actionPerformed(null);\r
- }\r
-\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new PIDColourScheme() );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme() );\r
- }\r
-\r
-\r
-\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
-\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelectionGroup().getSize()<2)\r
- JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
- else\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(new PairwiseAlignPanel(viewport));\r
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
- }\r
- }\r
-\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
- +"at least 4 input sequences.",\r
- "Sequence selection insufficient",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- try{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
-\r
- }\r
-\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
- }\r
-\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- //are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
- }\r
-\r
- addTreeMenuItem(tp, title);\r
-\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- }\r
-\r
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
- {\r
- final JMenuItem item = new JMenuItem(title);\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- alignPanel.repaint();\r
- }\r
- });\r
-\r
- treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- sortByTreeMenu.remove(item);\r
- };\r
- });\r
-\r
- }\r
-\r
-\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
- "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
- +" Nucleic Acids Research, submitted, June 1994.",\r
- 450, 150);\r
-\r
- ClustalThread thread = new ClustalThread(info);\r
- thread.start();\r
- }\r
-\r
- class ClustalThread extends Thread\r
- {\r
- WebserviceInfo info;\r
- public ClustalThread(WebserviceInfo info)\r
- {this.info = info; }\r
-\r
- public void run()\r
- {\r
- info.setStatus(WebserviceInfo.STATE_RUNNING);\r
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
- Vector sv = viewport.getAlignment().getSequences();\r
- SequenceI[] seqs = new SequenceI[sv.size()];\r
-\r
- int i = 0;\r
- do\r
- {\r
- seqs[i] = (SequenceI) sv.elementAt(i);\r
- }\r
- while (++i < sv.size());\r
-\r
- SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
- if (alignment != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(alignment));\r
- Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
- NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- af.clustalColour_actionPerformed(null);\r
- af.clustalColour.setSelected(true);\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
- {\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- info.appendProgressText("Problem obtaining clustal alignment");\r
- }\r
- }\r
- }\r
-\r
- protected void jpred_actionPerformed(ActionEvent e)\r
-{\r
-\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
- {\r
- JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
- }\r
- else\r
- {\r
- int sz;\r
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
-\r
- JPredClient ct = new JPredClient(msa);\r
- }\r
-\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
- {\r
- JPredClient ct = new JPredClient( (SequenceI)\r
- seqs.elementAt(0));\r
- }\r
- else\r
- {\r
- SequenceI[] msa = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- JPredClient ct = new JPredClient(msa);\r
- }\r
-\r
- }\r
- }\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
-\r
- MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1) {\r
- SequenceI[] msa = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- MsaWSClient ct = new MsaWSClient(msa);\r
- }\r
-\r
- }\r
- }\r
-\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
- // Pick the tree file\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select a newick-like tree file");\r
- chooser.setToolTipText("Load a tree file");\r
- int value = chooser.showOpenDialog(null);\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
- ShowNewickTree(fin, choice);\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "Problem reading tree file",\r
- ex.getMessage(),\r
- JOptionPane.WARNING_MESSAGE);\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public void ShowNewickTree(NewickFile nf, String title)\r
- {\r
- try{\r
- nf.parse();\r
- if (nf.getTree() != null)\r
- {\r
- TreePanel tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(),\r
- nf, "FromFile", title);\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
- }\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
-\r
-}\r
+/********************
+ * 2004 Jalview Reengineered
+ * Barton Group
+ * Dundee University
+ *
+ * AM Waterhouse
+ *******************/
+
+
+
+
+package jalview.gui;
+
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.*;
+import jalview.datamodel.*;
+import jalview.analysis.*;
+import jalview.io.*;
+import jalview.ws.*;
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import java.util.*;
+import java.awt.datatransfer.*;
+
+
+public class AlignFrame extends GAlignFrame
+{
+ final AlignmentPanel alignPanel;
+ final AlignViewport viewport;
+ public static final int NEW_WINDOW_WIDTH = 700;
+ public static final int NEW_WINDOW_HEIGHT = 500;
+ public String currentFileFormat = "Jalview";
+
+ public AlignFrame(AlignmentI al)
+ {
+ viewport = new AlignViewport(al);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+ alignPanel.annotationPanel.adjustPanelHeight();
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+ alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
+
+ getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameActivated(InternalFrameEvent evt)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ { alignPanel.requestFocus(); }
+ });
+
+ }
+ });
+
+ }
+
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
+ , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
+ new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+ currentFileFormat);
+
+ chooser.setAcceptAllFileFilterUsed(false);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Alignment to file");
+ chooser.setToolTipText("Save");
+ int value = chooser.showSaveDialog(this);
+ if(value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ currentFileFormat = chooser.getSelectedFormat();
+
+ if (currentFileFormat.equals("Jalview"))
+ {
+ String shortName = title.replace('/', '_');
+ title = title.replace('\\', '_');
+ String choice = chooser.getSelectedFile().getPath();
+ Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
+ choice);
+ // USE Jalview2XML to save this file
+ return;
+ }
+
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
+ try{
+ java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
+ out.println(output);
+ out.close();
+ }
+ catch(Exception ex){}
+ }
+
+ }
+
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+ JInternalFrame frame = new JInternalFrame();
+ cap.formatForOutput();
+ frame.setContentPane(cap);
+ Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
+ cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
+ }
+
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ HTMLOutput htmlOutput = new HTMLOutput(viewport);
+ htmlOutput = null;
+ }
+
+ protected void createPNG_actionPerformed(ActionEvent e)
+ {
+ alignPanel.makePNG();
+ }
+
+ protected void epsFile_actionPerformed(ActionEvent e)
+ {
+ alignPanel.makeEPS();
+ }
+
+
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread();
+ thread.start();
+ }
+
+ class PrintThread extends Thread
+ {
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ printJob.setPrintable(alignPanel, pf);
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+
+ }
+
+
+
+
+ public void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+ try{
+ this.setClosed(true);
+ }catch(Exception ex){}
+ }
+
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+
+ void updateEditMenuBar()
+ {
+ if(historyList.size()>0)
+ {
+ undoMenuItem.setEnabled(true);
+ Object [] history = (Object[])historyList.get(0);
+ undoMenuItem.setText("Undo "+history[0]);
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ }
+
+ if(redoList.size()>0)
+ {
+ redoMenuItem.setEnabled(true);
+ Object [] history = (Object[])redoList.get(0);
+ redoMenuItem.setText("Redo "+history[0]);
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ }
+ }
+
+ public void addHistoryItem(String type)
+ {
+ // must make sure we add new sequence objects her, not refs to the existing sequences
+ redoList.clear();
+
+ SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
+ for(int i=0; i<viewport.getAlignment().getHeight(); i++)
+ {
+ seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
+ viewport.getAlignment().getSequenceAt(i).getSequence());
+ }
+
+
+ historyList.add(0, new Object[]{type, seq} );
+ updateEditMenuBar();
+ }
+
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ Object [] history = (Object[])historyList.remove(0);
+ // add the redo state before continuing!!
+ SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+ {
+ seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
+ viewport.getAlignment().getSequenceAt(i).
+ getSequence());
+ }
+ /////////
+
+ redoList.add(0, new Object[] {history[0], seq});
+
+ seq = (SequenceI[]) history[1];
+ AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
+ viewport.setAlignment( new Alignment(seq) );
+ viewport.alignment.setGapCharacter( Preferences.gapSymbol );
+ updateEditMenuBar();
+ for(int i=0; i<old.length; i++)
+ viewport.alignment.addAnnotation(old[i]);
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ alignPanel.repaint();
+ }
+
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ return;
+
+ if (up)
+ {
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.sequences.contains(seq))
+ continue;
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+ if (sg.sequences.contains(temp))
+ continue;
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);
+ }
+ }
+ else
+ {
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.sequences.contains(seq))
+ continue;
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+ if (sg.sequences.contains(temp))
+ continue;
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ alignPanel.repaint();
+ }
+
+
+
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getSelectionGroup()==null)
+ return;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ StringBuffer buffer= new StringBuffer();
+
+ Hashtable orderedSeqs = new Hashtable();
+ for(int i=0; i<sg.getSize(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.alignment.findIndex(seq);
+ orderedSeqs.put(index+"", seq);
+ }
+
+ int index=0;
+ for(int i=0; i<sg.getSize(); i++)
+ {
+ SequenceI seq = null;
+ while( seq == null )
+ {
+ if(orderedSeqs.containsKey(index+""))
+ {
+ seq = (SequenceI) orderedSeqs.get(index + "");
+ index++;
+ break;
+ }
+ else
+ index++;
+ }
+
+ buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
+ +seq.findPosition( sg.getEndRes() )+ "\t"
+ +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
+ }
+ c.setContents( new StringSelection( buffer.toString()) , null ) ;
+
+ }
+
+
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ paste(true);
+ }
+
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("Paste");
+ paste(false);
+ }
+
+ void paste(boolean newAlignment)
+ {
+ try{
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+ if (contents == null)
+ return;
+
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ StringTokenizer st = new StringTokenizer(str);
+ ArrayList seqs = new ArrayList();
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+ int start = Integer.parseInt(st.nextToken());
+ int end = Integer.parseInt(st.nextToken());
+ Sequence sequence = new Sequence(name,st.nextToken(), start, end);
+
+ if(!newAlignment)
+ viewport.alignment.addSequence(sequence);
+ else
+ seqs.add(sequence);
+ }
+
+ if(newAlignment)
+ {
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];
+ seqs.toArray(newSeqs);
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+ String newtitle = new String("Copied sequences");
+ if( title.startsWith("Copied sequences"))
+ newtitle = title;
+ else
+ newtitle = newtitle.concat("- from "+title);
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+ }
+ else
+ {
+ viewport.setEndSeq(viewport.alignment.getHeight());
+ viewport.alignment.getWidth();
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+ }catch(Exception ex){}// could be anything being pasted in here
+
+ }
+
+
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("Delete");
+ if (viewport.getSelectionGroup() == null)
+ return;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i=0;i < sg.sequences.size(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.getAlignment().findIndex(seq);
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+
+ if(seq.getSequence().length()<1)
+ viewport.getAlignment().deleteSequence(seq);
+ else
+ viewport.getAlignment().getSequences().setElementAt(seq, index);
+ }
+
+ viewport.setSelectionGroup(null);
+ viewport.alignment.deleteGroup(sg);
+ viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
+ if(viewport.getAlignment().getHeight()<1)
+ try
+ {
+ this.setClosed(true);
+ }catch(Exception ex){}
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+
+ }
+
+
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ Object [] history = (Object[])redoList.remove(0);
+ SequenceI[] seq = (SequenceI[]) history[1];
+ viewport.setAlignment( new Alignment(seq) );
+ viewport.alignment.setGapCharacter( Preferences.gapSymbol );
+ updateEditMenuBar();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ alignPanel.repaint();
+ }
+
+
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.setSelectionGroup(null);
+ alignPanel.repaint();
+ }
+
+
+
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+ sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+ sg.setEndRes(viewport.alignment.getWidth());
+ viewport.setSelectionGroup(sg);
+ PaintRefresher.Refresh(null);
+ }
+
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ PaintRefresher.Refresh(null);
+ }
+
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+ sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
+ PaintRefresher.Refresh(null);
+ }
+
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("delete columns");
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel.size() > 0)
+ {
+ int min = colSel.getMin();
+ viewport.getAlignment().trimLeft(min);
+ colSel.compensateForEdit(0,min);
+
+ if(viewport.getSelectionGroup()!=null)
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+ if(!sg.adjustForRemoveLeft(min))
+ viewport.alignment.deleteGroup(sg);
+ }
+
+ alignPanel.repaint();
+ }
+ }
+
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("delete columns");
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel.size() > 0)
+ {
+ int max = colSel.getMax();
+ viewport.getAlignment().trimRight(max);
+ if(viewport.getSelectionGroup()!=null)
+ viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+ if(!sg.adjustForRemoveRight(max))
+ viewport.alignment.deleteGroup(sg);
+ }
+
+
+
+ alignPanel.repaint();
+ }
+
+ }
+
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("delete gapped columns");
+ viewport.getAlignment().removeGaps();
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("delete all gaps");
+ SequenceI current;
+ int jSize;
+ for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+ jSize = current.getLength();
+ for (int j=0; j < jSize; j++)
+ if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ current.deleteCharAt(j);
+ j--;
+ jSize--;
+ }
+ }
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame frame = new JInternalFrame();
+ Finder finder = new Finder(viewport, alignPanel, frame);
+ frame.setContentPane(finder);
+ Desktop.addInternalFrame(frame, "Find", 340,110);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+
+ }
+
+
+ public void font_actionPerformed(ActionEvent e)
+ {
+ FontChooser fc = new FontChooser( alignPanel );
+ }
+
+ protected void fullSeqId_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowFullId( fullSeqId.isSelected() );
+
+ alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+ alignPanel.repaint();
+ }
+
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText( colourTextMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+ alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+ scaleAbove.setVisible( wrapMenuItem.isSelected() );
+ scaleLeft.setVisible( wrapMenuItem.isSelected() );
+ scaleRight.setVisible( wrapMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.repaint();
+ }
+
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.repaint();
+ }
+
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.repaint();
+ }
+
+
+
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText( viewTextMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+ if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+ {
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
+ ((Alignment)viewport.alignment).featuresAdded = true;
+ }
+ alignPanel.repaint();
+ }
+
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+ {
+ annotationPanelMenuItem.setSelected(false);
+ return;
+ }
+ viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+ alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
+ }
+
+ public void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (alignPanel.overviewPanel != null)
+ return;
+
+ JInternalFrame frame = new JInternalFrame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.setContentPane(overview);
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ frame.getWidth(), frame.getHeight());
+ frame.pack();
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
+
+ alignPanel.setOverviewPanel( overview );
+
+
+ }
+
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ changeColour( null );
+ }
+
+
+ public void clustalColour_actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold.setSelected(false);
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+
+
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ changeColour( new HydrophobicColourScheme() );
+ }
+
+ public void helixColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HelixColourScheme() );
+ }
+
+
+ public void strandColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new StrandColourScheme());
+ }
+
+
+ public void turnColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TurnColourScheme());
+ }
+
+
+ public void buriedColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new BuriedColourScheme() );
+ }
+
+ public void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+
+
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+
+
+ void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if ( viewport.getAbovePIDThreshold() )
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+
+ if (cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) cs).setThreshold(threshold);
+ else if (cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) cs).setThreshold(threshold);
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else if (cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) cs).setThreshold(0);
+ else if (cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) cs).setThreshold(0);
+
+
+
+ if (viewport.getConservationSelected())
+ {
+ ConservationColourScheme ccs = null;
+
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ ccs = new ConservationColourScheme(c, cs);
+
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ ccs.setConsensus( viewport.vconsensus );
+ viewport.setGlobalColourScheme(ccs);
+
+ SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+
+ }
+ else
+ {
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ if (cs != null)
+ cs.setConsensus(viewport.vconsensus);
+ viewport.setGlobalColourScheme(cs);
+ }
+
+
+ if(viewport.getColourAppliesToAllGroups())
+ {
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+ }
+ else if(cs!=null)
+ {
+ try{
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ }catch(Exception ex){ex.printStackTrace();}
+ }
+
+ if(viewport.getAbovePIDThreshold())
+ {
+ if (sg.cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+ else if (sg.cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+
+ sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+ }
+
+ if( viewport.getConservationSelected() )
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.sequences, 0, viewport.alignment.getWidth()-1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+ sg.cs = ccs;
+ }
+ else if(cs!=null)
+ {
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+ }
+
+ }
+ }
+
+ if(alignPanel.getOverviewPanel()!=null)
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ alignPanel.repaint();
+ }
+
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+ "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+ "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setSelected(false);
+
+ ColourSchemeI cs = viewport.getGlobalColourScheme();
+ if(cs instanceof ConservationColourScheme )
+ changeColour( ((ConservationColourScheme)cs).cs );
+ else
+ changeColour( cs );
+
+ modifyConservation_actionPerformed(null);
+ }
+
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+ conservationMenuItem.setSelected(false);
+ viewport.setConservationSelected(false);
+
+ ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+ if(cs instanceof ConservationColourScheme )
+ changeColour( ((ConservationColourScheme)cs).cs );
+ else
+ changeColour( cs );
+
+ modifyPID_actionPerformed(null);
+ }
+
+
+
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+ }
+
+ public void PIDColour_actionPerformed(ActionEvent e)
+ {
+ changeColour( new PIDColourScheme() );
+ }
+
+
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new Blosum62ColourScheme() );
+ }
+
+
+
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("sort");
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
+ alignPanel.repaint();
+ }
+
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("sort");
+ AlignmentSorter.sortByID( viewport.getAlignment() );
+ alignPanel.repaint();
+ }
+
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("sort");
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ AlignmentSorter.sortGroups(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ RedundancyPanel sp = new RedundancyPanel(alignPanel);
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(sp);
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
+
+ }
+
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getSelectionGroup().getSize()<2)
+ JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+ else
+ {
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(new PairwiseAlignPanel(viewport));
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ }
+ }
+
+ public void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
+ || viewport.getAlignment().getHeight()<4)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
+ +"at least 4 input sequences.",
+ "Sequence selection insufficient",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ try{
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(pcaPanel);
+ Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
+ }catch(java.lang.OutOfMemoryError ex)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
+ "Out of memory", JOptionPane.WARNING_MESSAGE);
+ }
+
+
+ }
+
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+ }
+
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ //are the sequences aligned?
+ if(!viewport.alignment.isAligned())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
+ "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ final TreePanel tp;
+ if (viewport.getSelectionGroup() != null &&
+ viewport.getSelectionGroup().getSize() > 3)
+ {
+ tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+ pwType,
+ 0, viewport.alignment.getWidth());
+ }
+ else
+ {
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+ type, pwType, 0, viewport.alignment.getWidth());
+ }
+
+ addTreeMenuItem(tp, title);
+
+ Desktop.addInternalFrame(tp, title, 600, 500);
+ }
+
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
+ final JMenuItem item = new JMenuItem(title);
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("sort");
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+ alignPanel.repaint();
+ }
+ });
+ }
+
+ void addTreeMenuItem(final TreePanel treePanel, String title)
+ {
+ final JMenuItem item = new JMenuItem(title);
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem("sort");
+ AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+ alignPanel.repaint();
+ }
+ });
+
+ treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+ {
+ sortByTreeMenu.remove(item);
+ };
+ });
+
+ }
+
+
+ public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
+ }
+ }
+/* Old cLustalW
+ WebserviceInfo info = new WebserviceInfo("Clustal web service",
+ "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ +" Nucleic Acids Research, submitted, June 1994.",
+ 450, 150);
+
+ ClustalThread thread = new ClustalThread(info);
+ thread.start();
+ }
+
+ class ClustalThread extends Thread
+ {
+ WebserviceInfo info;
+ public ClustalThread(WebserviceInfo info)
+ {this.info = info; }
+
+ public void run()
+ {
+ info.setStatus(WebserviceInfo.STATE_RUNNING);
+ jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+ Vector sv = viewport.getAlignment().getSequences();
+ SequenceI[] seqs = new SequenceI[sv.size()];
+
+ int i = 0;
+ do
+ {
+ seqs[i] = (SequenceI) sv.elementAt(i);
+ }
+ while (++i < sv.size());
+
+ SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+ if (alignment != null)
+ {
+ AlignFrame af = new AlignFrame(new Alignment(alignment));
+ Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
+ NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+ af.clustalColour_actionPerformed(null);
+ af.clustalColour.setSelected(true);
+ info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else
+ {
+ info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ info.appendProgressText("Problem obtaining clustal alignment");
+ }
+ }
+ }
+*/
+
+ protected void jpred_actionPerformed(ActionEvent e)
+{
+
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+ {
+ JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+ }
+ else
+ {
+ int sz;
+ SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+ JPredClient ct = new JPredClient(msa);
+ }
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() == 1 || !viewport.alignment.isAligned())
+ {
+ JPredClient ct = new JPredClient( (SequenceI)
+ seqs.elementAt(0));
+ }
+ else
+ {
+ SequenceI[] msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ JPredClient ct = new JPredClient(msa);
+ }
+
+ }
+ }
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
+ }
+ }
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select a newick-like tree file");
+ chooser.setToolTipText("Load a tree file");
+ int value = chooser.showOpenDialog(null);
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ try
+ {
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
+ ShowNewickTree(fin, choice);
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Problem reading tree file",
+ ex.getMessage(),
+ JOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void ShowNewickTree(NewickFile nf, String title)
+ {
+ try{
+ nf.parse();
+ if (nf.getTree() != null)
+ {
+ TreePanel tp = new TreePanel(viewport,
+ viewport.getAlignment().getSequences(),
+ nf, "FromFile", title);
+ Desktop.addInternalFrame(tp, title, 600, 500);
+ addTreeMenuItem(tp, title);
+ viewport.setCurrentTree(tp.getTree());
+ }
+ }catch(Exception ex){ex.printStackTrace();}
+ }
+
+
+}
git://source.jalview.org / jalview.git / commitdiff