import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.gui.*;
String tmpPDBFile;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
this.pdbentry = pdbentry;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.io.FileParse;
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
{
char base = line.charAt(i);
- if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D'))
+ if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D')|| (base == '1')|| (base == 'F')|| (base == 'G')|| (base == '2')|| (base == 'I')|| (base == 'J')|| (base == 'K')|| (base == 'L')|| (base == 'M')|| (base == 'N')|| (base == 'O')|| (base == 'P')|| (base == 'Q')|| (base == 'R')|| (base == 'S')|| (base == 'T')|| (base == 'U')|| (base == 'V')|| (base == 'W')|| (base == 'X')|| (base == 'Y')|| (base == 'Z'))
{
stack.push(i);
}
- else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd'))
+ else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd')|| (base == 'e')|| (base == 'f')|| (base == 'g')|| (base == 'h')|| (base == 'i')|| (base == 'j')|| (base == 'k')|| (base == 'l')|| (base == 'm')|| (base == 'n')|| (base == 'o')|| (base == 'p')|| (base == 'q')|| (base == 'r')|| (base == 's')|| (base == 't')|| (base == 'u')|| (base == 'v')|| (base == 'w')|| (base == 'x')|| (base == 'y')|| (base == 'z'))
{
}
Object temp = stack.pop();
pairs.addElement(temp);
- pairs.addElement(i);
+ pairs.addElement(i);
+ //System.out.println(pairs);
}
i++;
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+ System.out.print("indice"+indice+" ");
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
+ System.out.println(pairs[i].getEnd());
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+// System.out.println("longueur="+sequences.length);
+// for(int l=0;l<=(sequences.length-1);l++){
+// System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString());
+// }
+// System.out.println("start="+start);
+ System.out.println("end="+end);
+// System.out.println("result="+result.length);
+//
+// System.out.println("profile="+profile);
+// System.out.println("rnaStruc="+rnaStruc);
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ //System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
+
}
else
{
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
+
bpEnd = findPair(rna, i);
+
if (bpEnd>-1)
{
for (j = 0; j < jSize; j++) // foreach row
continue;
}
c = sequences[j].getCharAt(i);
- {
+ //System.out.println("c="+c);
+
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
continue;
}
cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
+
+
+ System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd)==true)
{
values['(']++; // H means it's a helix (structured)
+ maxResidue = "(";
+ wooble=true;
+ System.out.println("It's a pair wc");
+
}
- pairs[c][cEnd]++;
-
- maxResidue = "(";
- }
- }
+ if (checkBpType(c, cEnd)==false)
+ {
+ wooble =false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+ System.out.println("It's an pair non canonic");
+ System.out.println(sequences[j].getRNA());
+ System.out.println(rnaStruc.getRNAStruc().charAt(i));
+ }
+ pairs[c][cEnd]++;
+
+
+ }
}
// nonGap++;
}
residueHash.put(PAIRPROFILE, pairs);
}
-
+ if (wooble==true)
+ {
count = values['('];
-
+ }
+ if (wooble==false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
}
if (bpEnd > 0)
{
- values[')'] = values['('];
+ values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble==true){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if(wooble==false){
+ System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
\r
public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
{\r
* @throws ExceptionLoadingFailed \r
* @throws ExceptionPermissionDenied \r
* @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
*/\r
- public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {\r
+ public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {\r
\r
TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
if( !file.isValid()) {\r
*/
package jalview.bin;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
}
});
}
+ protected static boolean proteine;
/**
* main class for Jalview application
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
+
+ JFrame Typechooser =new JFrame("choose molecule type");
+ FlowLayout fl = new FlowLayout();
+ Typechooser.setLayout(fl);
+ Typechooser.setSize(400,400);
+ Typechooser.setDefaultCloseOperation(Typechooser.DISPOSE_ON_CLOSE);
+ JLabel label = new JLabel("What would you open ? ");
+ JButton rnabutton = new JButton("RNA molecule");
+ JButton pbutton = new JButton("Proteine molecule");
+
+ pbutton.addActionListener(new pbuttonlistener());
+ rnabutton.addActionListener(new rnabuttonlistener());
+ Typechooser.getContentPane().add(label);
+ Typechooser.getContentPane().add(rnabutton);
+ Typechooser.getContentPane().add(pbutton);
+ Typechooser.setVisible(true);
+
+
+
+
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true)
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar");
desktop.setInBatchMode(false);
}
}
-
+
+
private static void startUsageStats(final Desktop desktop)
{
/**
* @author Andrew Waterhouse and JBP documented.
*
*/
+
+class rnabuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+ System.out.println("Good idea ! ");
+
+ }
+}
+
+class pbuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+
+
+ }
+}
+
class ArgsParser
{
Vector vargs = null;
{
return queued == 0 && running == 0;
}
+
+
+
};
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S'
- || annotations[i].secondaryStructure == 'C')
+ //System.out.println(annotations[i].secondaryStructure);
+ if (annotations[i].secondaryStructure == '('
+ || annotations[i].secondaryStructure == '['
+ || annotations[i].secondaryStructure == '<'
+ || annotations[i].secondaryStructure == '{'
+ || annotations[i].secondaryStructure == 'A'
+ || annotations[i].secondaryStructure == 'B'
+ || annotations[i].secondaryStructure == 'C'
+ || annotations[i].secondaryStructure == 'D'
+ || annotations[i].secondaryStructure == '1'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == '2'
+ || annotations[i].secondaryStructure == 'I'
+ || annotations[i].secondaryStructure == 'J'
+ || annotations[i].secondaryStructure == 'K'
+ || annotations[i].secondaryStructure == 'L'
+ || annotations[i].secondaryStructure == 'M'
+ || annotations[i].secondaryStructure == 'N'
+ || annotations[i].secondaryStructure == 'O'
+ || annotations[i].secondaryStructure == 'P'
+ || annotations[i].secondaryStructure == 'Q'
+ || annotations[i].secondaryStructure == 'R'
+ || annotations[i].secondaryStructure == 'S'
+ || annotations[i].secondaryStructure == 'T'
+ || annotations[i].secondaryStructure == 'U'
+ || annotations[i].secondaryStructure == 'V'
+ || annotations[i].secondaryStructure == 'W'
+ || annotations[i].secondaryStructure == 'X'
+ || annotations[i].secondaryStructure == 'Y'
+ || annotations[i].secondaryStructure == 'Z')
{
hasIcons |= true;
isrna |= true;
firstChar != ' '
&& firstChar != 'H'
&& firstChar != 'E'
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
+ && firstChar != '1'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != '2'
+ && firstChar != 'I'
+ && firstChar != 'J'
+ && firstChar != 'K'
+ && firstChar != 'L'
+ && firstChar != 'M'
+ && firstChar != 'N'
+ && firstChar != 'O'
+ && firstChar != 'P'
+ && firstChar != 'Q'
+ && firstChar != 'R'
&& firstChar != 'S'
+ && firstChar != 'T'
+ && firstChar != 'U'
+ && firstChar != 'V'
+ && firstChar != 'W'
+ && firstChar != 'X'
+ && firstChar != 'Y'
+ && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
*/\r
public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
{\r
+ \r
ArrayList<String> str = new ArrayList<String>();\r
StringBuffer command = new StringBuffer();\r
\r
AlignmentPanel ap;
- public AppVarna(String sname, SequenceI seq, String strucseq, RNA struc,
+ public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
String name, AlignmentPanel ap)
{
-
-
+ System.out.println("je suis là (AppVarna!!");
+ System.out.println("1:"+sname);
+ System.out.println("2:"+seq);
+ System.out.println("3:"+strucseq);
+ System.out.println("4:"+struc);
+ System.out.println("5:"+name);
+ System.out.println("6:"+ap);
this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
- System.out.println(struc);
- RNA rna1 = new RNA(struc);
- rna1.setName(name);
- rna1.restrictTo(strucseq);
- /*try
+ RNA rna1 = new RNA(name);
+ try
{
- System.err.println(struc + "->" + replaceOddGaps(struc));
+ System.out.println("ou ici ?");
rna1.setRNA(strucseq, replaceOddGaps(struc));
-
+ System.out.println("La séquence est :"+rna1.getSeq());
+ System.out.println("La séquence est :"+struc);
+ System.out.println("La séquence est :"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
} catch (ExceptionFileFormatOrSyntax e3)
{
e3.printStackTrace();
- }*/
+ }
RNA trim = trimRNA(rna1, "trimmed "+sname);
- //TODO: Use RNA.selectTo instead...
rnaList.add(trim);
rnaList.add(rna1);
public void initVarna()
{
-
+ System.out.println("initialisation VANRA");
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
getBounds().width, getBounds().height);
this.pack();
showPanel(true);
-
+ System.out.println("Sortie initialisation VANRA");
}
public String replaceOddGaps(String oldStr)
public AppVarnaBinding(ArrayList<RNA> rnaList)
{
-;
+
// super("VARNA in Jalview");
initVarnaEdit(rnaList);
}
public void onUINewStructure(VARNAConfig v, RNA r)
{
- //_rnaList.add(v, r, "", true);
+ _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
PDBEntry entry = new PDBEntry();
try
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import MCview.*;
import jalview.analysis.*;
//System.out.println("3:"+seq.getSequenceAsString());
System.out.println("3:strucseq"+rnastruc);
- System.out.println("4:struc"+seq.getRNA());
+ //System.out.println("4:struc"+seq.getRNA());
System.out.println("5:name"+seq.getName());
System.out.println("6:ap"+ap);
- new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
System.out.println("end");
}
});
{
// TODO: VARNA does'nt print gaps in the sequence
- new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(),
- seq.getName(), ap);
+ //new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+ new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
}
});
viewStructureMenu.add(menuItem);
} catch (InterruptedException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
+ } catch (ExceptionUnmatchedClosingParentheses e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
}
}
});
oal = null;
}
- public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
/**
* DOCUMENT ME!
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
initData();
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
initData();
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException;
+ public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
/**
* Print out in alignment file format the Sequences in the seqs Vector.
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
"sto,stk","xml" }; // ,
// ".blast"
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public BLCFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public BLCFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public BLCFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public BLCFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.util.*;
{
}
- public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public FastaFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public FastaFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public FastaFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public FastaFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
\r
import jalview.analysis.SequenceIdMatcher;\r
import jalview.datamodel.*;\r
* @throws ExceptionLoadingFailed \r
* @throws ExceptionPermissionDenied \r
* @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
*/\r
- public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(inFile, type);\r
}\r
\r
- public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(source);\r
}\r
break;
}
- if ((data.indexOf(">") > -1))
+ if ((data.indexOf("<") > -1))
{
reply = "RNAML";
- System.out.println("This is a RNAML format");
+
break;
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
try
{
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.util.*;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
{
}
- public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.util.*;
{
}
- public PfamFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PfamFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public PfamFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PfamFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.util.*;
* @throws ExceptionLoadingFailed
* @throws ExceptionPermissionDenied
* @throws InterruptedException
+ * @throws ExceptionUnmatchedClosingParentheses
*/
- public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
import fr.orsay.lri.varna.models.rna.RNA;
}
- public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
+ @SuppressWarnings("unchecked")
public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
{
FileReader fr = null;
fr = new FileReader(inFile);
BufferedReader r = new BufferedReader (fr);
- Hashtable seqhash = new Hashtable();
- Vector headers = new Vector();
+
//ArrayList<String> seq =new ArrayList();
//System.out.println(r);
result = RNAFactory.loadSecStrRNAML(r);
- System.out.println("this is the secondary scructure:" +result.toArray());
+ System.out.println("this is the secondary scructure:" +result.size());
//System.out.println("this is the secondary scructure:" +result.toString());
//System.out.println("this is the secondary scructure:" +result.size());
- for(int i=0;i<result.size();i++)
- {
- //System.out.println(result.get(0).getSeq());
- //System.out.println(result.get(0).getStructBPSEQ());
- //System.out.println(result.get(0).getStructDBN(true));
- String rna1 =result.get(0).getStructDBN(true);
- //System.out.println(result.get(0).getAnnotations());
- String seq = result.get(0).getSeq();
+ SequenceI[] seqs = new SequenceI[result.size()];
System.out.println(type); //the type is "File"
System.out.println(inFile );//inFile is the path
+
+ for(int i=0;i<result.size();i++)
+ {
+ RNA current = result.get(i);
+ System.out.println(current.getSeq());
+ //System.out.println(result.get(i).getStructBPSEQ());
+ System.out.println(result.get(i).getStructDBN(true));
+ System.out.println(i);
+ String rna =current.getStructDBN(true);
+ //System.out.println(result.get(0).getAnnotations());
+ String seq = current.getSeq();
+
int begin=0;
int end = seq.length()-1;
- SequenceI[] seqs = new SequenceI[1];
+
id = safeName(getDataName());
- seqs[0] = new Sequence(id, seq, begin, end);
- SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
- seqs[0].addSequenceFeature(feat);
- this.setSeqs(seqs);
+ seqs[i] = new Sequence(id, seq, begin, end);
+ //System.out.println(seq);
+ System.out.println("Rna is still "+rna);
+ //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
+ //seqs[i].addSequenceFeature(feat);
- String[] annot=new String[10000] ;
- Annotation[] ann = new Annotation[1000];
- for(int j=0;j<rna1.length();j++)
+ String[] annot=new String[rna.length()] ;
+ Annotation[] ann = new Annotation[rna.length()];
+
+ for(int j=0;j<rna.length();j++)
{
- annot[j] =rna1.substring(j,j+1);
- System.out.println(annot[j]);
+ annot[j] =rna.substring(j,j+1);
+
}
- for(int k=0;k<rna1.length();k++)
+ for(int k=0;k<rna.length();k++)
{
- ann[k] = new Annotation(annot[k], "", ' ', 0f);
-
- ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
-
+ ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
+
}
- AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
- seqs[0].addAlignmentAnnotation(align);
- seqs[0].setRNA(result.get(begin));
- this.annotations.addElement(align);
-
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ this.annotations.addElement(align);
}
+ this.setSeqs(seqs);
+
+
- //Annotate3D tintin = new Annotate3D();
-
- //System.out.println(tintin);
+
}
return annotations;
}
}
-
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.util.*;
{
}
- public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+import fr.orsay.lri.varna.factories.RNAFactory;\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
import jalview.datamodel.*;\r
import jalview.analysis.Rna;\r
\r
public class StockholmFile extends AlignFile\r
{\r
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
-\r
+ protected ArrayList<RNA> result;\r
+ public String id;\r
+ \r
public StockholmFile()\r
{\r
}\r
\r
- public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(inFile, type);\r
}\r
\r
- public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException\r
+ public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
{\r
super(source);\r
}\r
* \r
* @throws IOException\r
* If there is an error with the input file\r
+ * @throws ExceptionUnmatchedClosingParentheses \r
*/\r
- public void parse() throws IOException\r
+ public void parse() throws IOException, ExceptionUnmatchedClosingParentheses\r
{\r
- StringBuffer treeString = new StringBuffer();\r
- String treeName = null;\r
- // --------------- Variable Definitions -------------------\r
- String line;\r
- String version;\r
- // String id;\r
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
- Hashtable seqs = new Hashtable();\r
- Regex p, r, rend, s, x;\r
-\r
- // Temporary line for processing RNA annotation\r
- // String RNAannot = "";\r
-\r
- // ------------------ Parsing File ----------------------\r
- // First, we have to check that this file has STOCKHOLM format, i.e. the\r
- // first line must match\r
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
- if (!r.search(nextLine()))\r
- {\r
- throw new IOException(\r
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
- }\r
- else\r
- {\r
- version = r.stringMatched(1);\r
- // logger.debug("Stockholm version: " + version);\r
- }\r
-\r
- // We define some Regexes here that will be used regularily later\r
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
- // id/from/to\r
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
-\r
- // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
-\r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
-\r
- rend.optimize();\r
- p.optimize();\r
- s.optimize();\r
- r.optimize();\r
- x.optimize();\r
- openparen.optimize();\r
- closeparen.optimize();\r
-\r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.length() == 0)\r
- {\r
- continue;\r
- }\r
- if (rend.search(line))\r
- {\r
- // End of the alignment, pass stuff back\r
-\r
- this.noSeqs = seqs.size();\r
- // logger.debug("Number of sequences: " + this.noSeqs);\r
- Enumeration accs = seqs.keys();\r
- while (accs.hasMoreElements())\r
- {\r
- String acc = (String) accs.nextElement();\r
- // logger.debug("Processing sequence " + acc);\r
- String seq = (String) seqs.remove(acc);\r
- if (maxLength < seq.length())\r
- {\r
- maxLength = seq.length();\r
- }\r
- int start = 1;\r
- int end = -1;\r
- String sid = acc;\r
- /*\r
- * Retrieve hash of annotations for this accession\r
- * Associate Annotation with accession\r
- */\r
- Hashtable accAnnotations = null;\r
-\r
- if (seqAnn != null && seqAnn.containsKey(acc))\r
- {\r
- accAnnotations = (Hashtable) seqAnn.remove(acc);\r
- //TODO: add structures to sequence\r
- }\r
-\r
- // Split accession in id and from/to\r
- if (p.search(acc))\r
- {\r
- sid = p.stringMatched(1);\r
- start = Integer.parseInt(p.stringMatched(2));\r
- end = Integer.parseInt(p.stringMatched(3));\r
- }\r
- // logger.debug(sid + ", " + start + ", " + end);\r
-\r
- Sequence seqO = new Sequence(sid, seq, start, end);\r
- // Add Description (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
- {\r
- String desc = (String) accAnnotations.get("DE");\r
- seqO.setDescription((desc == null) ? "" : desc);\r
- }\r
- // Add DB References (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
- {\r
- String dbr = (String) accAnnotations.get("DR");\r
- if (dbr != null && dbr.indexOf(";") > -1)\r
- {\r
- String src = dbr.substring(0, dbr.indexOf(";"));\r
- String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
- // seqO.addDBRef(dbref);\r
- }\r
- } \r
- if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
- {\r
- Vector v = (Vector) accAnnotations.get("SS");\r
- \r
- for (int i = 0; i < v.size(); i++)\r
- {\r
- AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
- seqO.addAlignmentAnnotation(an);\r
- //annotations.add(an);\r
- }\r
- }\r
- \r
- Hashtable features = null;\r
- // We need to adjust the positions of all features to account for gaps\r
- try\r
- {\r
- features = (Hashtable) accAnnotations.remove("features");\r
- } catch (java.lang.NullPointerException e)\r
- {\r
- // loggerwarn("Getting Features for " + acc + ": " +\r
- // e.getMessage());\r
- // continue;\r
- }\r
- // if we have features\r
- if (features != null)\r
- {\r
- int posmap[] = seqO.findPositionMap();\r
- Enumeration i = features.keys();\r
- while (i.hasMoreElements())\r
- {\r
- // TODO: parse out secondary structure annotation as annotation\r
- // row\r
- // TODO: parse out scores as annotation row\r
- // TODO: map coding region to core jalview feature types\r
- String type = i.nextElement().toString();\r
- Hashtable content = (Hashtable) features.remove(type);\r
- Enumeration j = content.keys();\r
- while (j.hasMoreElements())\r
- {\r
- String desc = j.nextElement().toString();\r
- String ns = content.get(desc).toString();\r
- char[] byChar = ns.toCharArray();\r
- for (int k = 0; k < byChar.length; k++)\r
- {\r
- char c = byChar[k];\r
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
- // uses\r
- // '.'\r
- // for\r
- // feature\r
- // background\r
- {\r
- int new_pos = posmap[k]; // look up nearest seqeunce\r
- // position to this column\r
- SequenceFeature feat = new SequenceFeature(type, desc,\r
- new_pos, new_pos, 0f, null);\r
-\r
- seqO.addSequenceFeature(feat);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- }\r
- // garbage collect\r
-\r
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
- // + ": " + seq);\r
- this.seqs.addElement(seqO);\r
- }\r
- return; // finished parsing this segment of source\r
- }\r
- else if (!r.search(line))\r
- {\r
- // System.err.println("Found sequence line: " + line);\r
-\r
- // Split sequence in sequence and accession parts\r
- if (!x.search(line))\r
- {\r
- // logger.error("Could not parse sequence line: " + line);\r
- throw new IOException("Could not parse sequence line: " + line);\r
- }\r
- String ns = (String) seqs.get(x.stringMatched(1));\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += x.stringMatched(2);\r
-\r
- seqs.put(x.stringMatched(1), ns);\r
- }\r
- else\r
- {\r
- String annType = r.stringMatched(1);\r
- String annContent = r.stringMatched(2);\r
-\r
- // System.err.println("type:" + annType + " content: " + annContent);\r
-\r
- if (annType.equals("GF"))\r
- {\r
- /*\r
- * Generic per-File annotation, free text Magic features: #=GF NH\r
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
- * \r
- * Compulsory fields: ------------------\r
- * \r
- * AC Accession number: Accession number in form PFxxxxx.version or\r
- * PBxxxxxx. ID Identification: One word name for family. DE\r
- * Definition: Short description of family. AU Author: Authors of the\r
- * entry. SE Source of seed: The source suggesting the seed members\r
- * belong to one family. GA Gathering method: Search threshold to\r
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
- * and domain score of match in the full alignment. NC Noise Cutoff:\r
- * Highest sequence score and domain score of match not in full\r
- * alignment. TP Type: Type of family -- presently Family, Domain,\r
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
- * Alignment Method The order ls and fs hits are aligned to the model\r
- * to build the full align. // End of alignment.\r
- * \r
- * Optional fields: ----------------\r
- * \r
- * DC Database Comment: Comment about database reference. DR Database\r
- * Reference: Reference to external database. RC Reference Comment:\r
- * Comment about literature reference. RN Reference Number: Reference\r
- * Number. RM Reference Medline: Eight digit medline UI number. RT\r
- * Reference Title: Reference Title. RA Reference Author: Reference\r
- * Author RL Reference Location: Journal location. PI Previous\r
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
- * NL Location: Location of nested domains - sequence ID, start and\r
- * end of insert.\r
- * \r
- * Obsolete fields: ----------- AL Alignment method of seed: The\r
- * method used to align the seed members.\r
- */\r
- // Let's save the annotations, maybe we'll be able to do something\r
- // with them later...\r
- Regex an = new Regex("(\\w+)\\s*(.*)");\r
- if (an.search(annContent))\r
- {\r
- if (an.stringMatched(1).equals("NH"))\r
- {\r
- treeString.append(an.stringMatched(2));\r
- }\r
- else if (an.stringMatched(1).equals("TN"))\r
- {\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (getTreeCount() + 1);\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- treeName = an.stringMatched(2);\r
- treeString = new StringBuffer();\r
- }\r
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GS"))\r
- {\r
- // Generic per-Sequence annotation, free text\r
- /*\r
- * Pfam uses these features: Feature Description ---------------------\r
- * ----------- AC <accession> ACcession number DE <freetext>\r
- * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
- * LO <look> Look (Color, etc.)\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String content = s.stringMatched(3);\r
- // TODO: store DR in a vector.\r
- // TODO: store AC according to generic file db annotation.\r
- Hashtable ann;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- ann = new Hashtable();\r
- }\r
- ann.put(type, content);\r
- seqAnn.put(acc, ann);\r
- }\r
- else\r
- {\r
- throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else if (annType.equals("GC"))\r
- {\r
- // Generic per-Column annotation, exactly 1 char per column\r
- // always need a label.\r
- if (x.search(annContent))\r
- {\r
- // parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1),\r
- x.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GR"))\r
- {\r
- // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
- // column\r
- /*\r
- * Feature Description Markup letters ------- -----------\r
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
- * or after) [0-2]\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String seq = new String(s.stringMatched(3));\r
- String description = null;\r
- // Check for additional information about the current annotation\r
- // We use a simple string tokenizer here for speed\r
- StringTokenizer sep = new StringTokenizer(seq, " \t");\r
- description = sep.nextToken();\r
- if (sep.hasMoreTokens())\r
- {\r
- seq = sep.nextToken();\r
- }\r
- else\r
- {\r
- seq = description;\r
- description = new String();\r
- }\r
- // sequence id with from-to fields\r
-\r
- Hashtable ann;\r
- // Get an object with all the annotations for this sequence\r
- if (seqAnn.containsKey(acc))\r
- {\r
- // logger.debug("Found annotations for " + acc);\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new annotations holder for " + acc);\r
- ann = new Hashtable();\r
- seqAnn.put(acc, ann);\r
- }\r
- //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
- Hashtable features;\r
- // Get an object with all the content for an annotation\r
- if (ann.containsKey("features"))\r
- {\r
- // logger.debug("Found features for " + acc);\r
- features = (Hashtable) ann.get("features");\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new features holder for " + acc);\r
- features = new Hashtable();\r
- ann.put("features", features);\r
- }\r
-\r
- Hashtable content;\r
- if (features.containsKey(this.id2type(type)))\r
- {\r
- // logger.debug("Found content for " + this.id2type(type));\r
- content = (Hashtable) features.get(this.id2type(type));\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new content holder for " +\r
- // this.id2type(type));\r
- content = new Hashtable();\r
- features.put(this.id2type(type), content);\r
- }\r
- String ns = (String) content.get(description);\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += seq;\r
- content.put(description, ns);\r
-
- if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
- }\r
- else\r
- {\r
- System.err\r
- .println("Warning - couldn't parse sequence annotation row line:\n"\r
- + line);\r
- // throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else\r
- {\r
- throw new IOException("Unknown annotation detected: " + annType\r
- + " " + annContent);\r
- }\r
- }\r
- }\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (1 + getTreeCount());\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
+ FileReader fr = null;\r
+ fr = new FileReader(inFile); \r
+\r
+ BufferedReader r = new BufferedReader (fr);\r
+ result = RNAFactory.loadSecStrStockholm(r);\r
+ System.out.println("this is the secondary scructure:" +result.size());\r
+ SequenceI[] seqs = new SequenceI[result.size()];\r
+ System.out.println(type); //the type is "File"\r
+ System.out.println(inFile );//inFile is the path\r
+ for(int i=0;i<result.size();i++)\r
+ {\r
+ RNA current = result.get(i);\r
+ \r
+ System.out.println(current.getSeq());\r
+ //System.out.println(result.get(i).getStructBPSEQ());\r
+ System.out.println(result.get(i).getStructDBN(true));\r
+ System.out.println(i);\r
+ String rna =current.getStructDBN(true);\r
+ String seq = current.getSeq();\r
+ int begin=0;\r
+ int end = seq.length()-1;\r
+ id = safeName(getDataName());\r
+ seqs[i] = new Sequence(id, seq, begin, end);\r
+ String[] annot=new String[rna.length()] ;\r
+ Annotation[] ann = new Annotation[rna.length()];\r
+ for(int j=0;j<rna.length();j++)\r
+ {\r
+ annot[j] =rna.substring(j,j+1);\r
+ \r
+ }\r
+ \r
+ for(int k=0;k<rna.length();k++)\r
+ {\r
+ ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);\r
+ \r
+ }\r
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);\r
+ \r
+ seqs[i].addAlignmentAnnotation(align);\r
+ seqs[i].setRNA(result.get(i));\r
+ this.annotations.addElement(align);\r
+ }\r
+ this.setSeqs(seqs);\r
+ \r
}\r
-\r
+// r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
+ // if (!r.search(nextLine()))\r
+// {\r
+// throw new IOException(\r
+// "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
+// }\r
+// else\r
+// {\r
+// version = r.stringMatched(1);\r
+// // logger.debug("Stockholm version: " + version);\r
+// }\r
+//\r
+// // We define some Regexes here that will be used regularily later\r
+// rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
+// p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
+// // id/from/to\r
+// s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
+// r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
+// x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
+//\r
+// // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
+// Regex openparen = new Regex("(<|\\[)", "(");\r
+// Regex closeparen = new Regex("(>|\\])", ")");\r
+//\r
+// // Detect if file is RNA by looking for bracket types\r
+// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+//\r
+// rend.optimize();\r
+// p.optimize();\r
+// s.optimize();\r
+// r.optimize();\r
+// x.optimize();\r
+// openparen.optimize();\r
+// closeparen.optimize();\r
+//\r
+// while ((line = nextLine()) != null)\r
+// {\r
+// if (line.length() == 0)\r
+// {\r
+// continue;\r
+// }\r
+// if (rend.search(line))\r
+// {\r
+// // End of the alignment, pass stuff back\r
+//\r
+// this.noSeqs = seqs.size();\r
+// // logger.debug("Number of sequences: " + this.noSeqs);\r
+// Enumeration accs = seqs.keys();\r
+// while (accs.hasMoreElements())\r
+// {\r
+// String acc = (String) accs.nextElement();\r
+// // logger.debug("Processing sequence " + acc);\r
+// String seq = (String) seqs.remove(acc);\r
+// if (maxLength < seq.length())\r
+// {\r
+// maxLength = seq.length();\r
+// }\r
+// int start = 1;\r
+// int end = -1;\r
+// String sid = acc;\r
+// /*\r
+// * Retrieve hash of annotations for this accession\r
+// * Associate Annotation with accession\r
+// */\r
+// Hashtable accAnnotations = null;\r
+//\r
+// if (seqAnn != null && seqAnn.containsKey(acc))\r
+// {\r
+// accAnnotations = (Hashtable) seqAnn.remove(acc);\r
+// //TODO: add structures to sequence\r
+// }\r
+//\r
+// // Split accession in id and from/to\r
+// if (p.search(acc))\r
+// {\r
+// sid = p.stringMatched(1);\r
+// start = Integer.parseInt(p.stringMatched(2));\r
+// end = Integer.parseInt(p.stringMatched(3));\r
+// }\r
+// // logger.debug(sid + ", " + start + ", " + end);\r
+//\r
+// Sequence seqO = new Sequence(sid, seq, start, end);\r
+// // Add Description (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
+// {\r
+// String desc = (String) accAnnotations.get("DE");\r
+// seqO.setDescription((desc == null) ? "" : desc);\r
+// }\r
+// // Add DB References (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
+// {\r
+// String dbr = (String) accAnnotations.get("DR");\r
+// if (dbr != null && dbr.indexOf(";") > -1)\r
+// {\r
+// String src = dbr.substring(0, dbr.indexOf(";"));\r
+// String acn = dbr.substring(dbr.indexOf(";") + 1);\r
+// jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+// // seqO.addDBRef(dbref);\r
+// }\r
+// } \r
+// if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
+// {\r
+// Vector v = (Vector) accAnnotations.get("SS");\r
+// \r
+// for (int i = 0; i < v.size(); i++)\r
+// {\r
+// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
+// seqO.addAlignmentAnnotation(an);\r
+// //annotations.add(an);\r
+// }\r
+// }\r
+// \r
+// Hashtable features = null;\r
+// // We need to adjust the positions of all features to account for gaps\r
+// try\r
+// {\r
+// features = (Hashtable) accAnnotations.remove("features");\r
+// } catch (java.lang.NullPointerException e)\r
+// {\r
+// // loggerwarn("Getting Features for " + acc + ": " +\r
+// // e.getMessage());\r
+// // continue;\r
+// }\r
+// // if we have features\r
+// if (features != null)\r
+// {\r
+// int posmap[] = seqO.findPositionMap();\r
+// Enumeration i = features.keys();\r
+// while (i.hasMoreElements())\r
+// {\r
+// // TODO: parse out secondary structure annotation as annotation\r
+// // row\r
+// // TODO: parse out scores as annotation row\r
+// // TODO: map coding region to core jalview feature types\r
+// String type = i.nextElement().toString();\r
+// Hashtable content = (Hashtable) features.remove(type);\r
+// Enumeration j = content.keys();\r
+// while (j.hasMoreElements())\r
+// {\r
+// String desc = j.nextElement().toString();\r
+// String ns = content.get(desc).toString();\r
+// char[] byChar = ns.toCharArray();\r
+// for (int k = 0; k < byChar.length; k++)\r
+// {\r
+// char c = byChar[k];\r
+// if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
+// // uses\r
+// // '.'\r
+// // for\r
+// // feature\r
+// // background\r
+// {\r
+// int new_pos = posmap[k]; // look up nearest seqeunce\r
+// // position to this column\r
+// SequenceFeature feat = new SequenceFeature(type, desc,\r
+// new_pos, new_pos, 0f, null);\r
+//\r
+// seqO.addSequenceFeature(feat);\r
+// }\r
+// }\r
+// }\r
+//\r
+// }\r
+//\r
+// }\r
+// // garbage collect\r
+//\r
+// // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
+// // + ": " + seq);\r
+// this.seqs.addElement(seqO);\r
+// }\r
+// return; // finished parsing this segment of source\r
+// }\r
+// else if (!r.search(line))\r
+// {\r
+// // System.err.println("Found sequence line: " + line);\r
+//\r
+// // Split sequence in sequence and accession parts\r
+// if (!x.search(line))\r
+// {\r
+// // logger.error("Could not parse sequence line: " + line);\r
+// throw new IOException("Could not parse sequence line: " + line);\r
+// }\r
+// String ns = (String) seqs.get(x.stringMatched(1));\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += x.stringMatched(2);\r
+//\r
+// seqs.put(x.stringMatched(1), ns);\r
+// }\r
+// else\r
+// {\r
+// String annType = r.stringMatched(1);\r
+// String annContent = r.stringMatched(2);\r
+//\r
+// // System.err.println("type:" + annType + " content: " + annContent);\r
+//\r
+// if (annType.equals("GF"))\r
+// {\r
+// /*\r
+// * Generic per-File annotation, free text Magic features: #=GF NH\r
+// * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
+// * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
+// * \r
+// * Compulsory fields: ------------------\r
+// * \r
+// * AC Accession number: Accession number in form PFxxxxx.version or\r
+// * PBxxxxxx. ID Identification: One word name for family. DE\r
+// * Definition: Short description of family. AU Author: Authors of the\r
+// * entry. SE Source of seed: The source suggesting the seed members\r
+// * belong to one family. GA Gathering method: Search threshold to\r
+// * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
+// * and domain score of match in the full alignment. NC Noise Cutoff:\r
+// * Highest sequence score and domain score of match not in full\r
+// * alignment. TP Type: Type of family -- presently Family, Domain,\r
+// * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
+// * Alignment Method The order ls and fs hits are aligned to the model\r
+// * to build the full align. // End of alignment.\r
+// * \r
+// * Optional fields: ----------------\r
+// * \r
+// * DC Database Comment: Comment about database reference. DR Database\r
+// * Reference: Reference to external database. RC Reference Comment:\r
+// * Comment about literature reference. RN Reference Number: Reference\r
+// * Number. RM Reference Medline: Eight digit medline UI number. RT\r
+// * Reference Title: Reference Title. RA Reference Author: Reference\r
+// * Author RL Reference Location: Journal location. PI Previous\r
+// * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
+// * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
+// * NL Location: Location of nested domains - sequence ID, start and\r
+// * end of insert.\r
+// * \r
+// * Obsolete fields: ----------- AL Alignment method of seed: The\r
+// * method used to align the seed members.\r
+// */\r
+// // Let's save the annotations, maybe we'll be able to do something\r
+// // with them later...\r
+// Regex an = new Regex("(\\w+)\\s*(.*)");\r
+// if (an.search(annContent))\r
+// {\r
+// if (an.stringMatched(1).equals("NH"))\r
+// {\r
+// treeString.append(an.stringMatched(2));\r
+// }\r
+// else if (an.stringMatched(1).equals("TN"))\r
+// {\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (getTreeCount() + 1);\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// treeName = an.stringMatched(2);\r
+// treeString = new StringBuffer();\r
+// }\r
+// setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GS"))\r
+// {\r
+// // Generic per-Sequence annotation, free text\r
+// /*\r
+// * Pfam uses these features: Feature Description ---------------------\r
+// * ----------- AC <accession> ACcession number DE <freetext>\r
+// * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
+// * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
+// * LO <look> Look (Color, etc.)\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String content = s.stringMatched(3);\r
+// // TODO: store DR in a vector.\r
+// // TODO: store AC according to generic file db annotation.\r
+// Hashtable ann;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// ann = new Hashtable();\r
+// }\r
+// ann.put(type, content);\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else if (annType.equals("GC"))\r
+// {\r
+// // Generic per-Column annotation, exactly 1 char per column\r
+// // always need a label.\r
+// if (x.search(annContent))\r
+// {\r
+// // parse out and create alignment annotation directly.\r
+// parseAnnotationRow(annotations, x.stringMatched(1),\r
+// x.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GR"))\r
+// {\r
+// // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
+// // column\r
+// /*\r
+// * Feature Description Markup letters ------- -----------\r
+// * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
+// * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
+// * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
+// * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
+// * or after) [0-2]\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String seq = new String(s.stringMatched(3));\r
+// String description = null;\r
+// // Check for additional information about the current annotation\r
+// // We use a simple string tokenizer here for speed\r
+// StringTokenizer sep = new StringTokenizer(seq, " \t");\r
+// description = sep.nextToken();\r
+// if (sep.hasMoreTokens())\r
+// {\r
+// seq = sep.nextToken();\r
+// }\r
+// else\r
+// {\r
+// seq = description;\r
+// description = new String();\r
+// }\r
+// // sequence id with from-to fields\r
+//\r
+// Hashtable ann;\r
+// // Get an object with all the annotations for this sequence\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// // logger.debug("Found annotations for " + acc);\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new annotations holder for " + acc);\r
+// ann = new Hashtable();\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
+// Hashtable features;\r
+// // Get an object with all the content for an annotation\r
+// if (ann.containsKey("features"))\r
+// {\r
+// // logger.debug("Found features for " + acc);\r
+// features = (Hashtable) ann.get("features");\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new features holder for " + acc);\r
+// features = new Hashtable();\r
+// ann.put("features", features);\r
+// }\r
+//\r
+// Hashtable content;\r
+// if (features.containsKey(this.id2type(type)))\r
+// {\r
+// // logger.debug("Found content for " + this.id2type(type));\r
+// content = (Hashtable) features.get(this.id2type(type));\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new content holder for " +\r
+// // this.id2type(type));\r
+// content = new Hashtable();\r
+// features.put(this.id2type(type), content);\r
+// }\r
+// String ns = (String) content.get(description);\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += seq;\r
+// content.put(description, ns);\r
+//
+// if(type.equals("SS")){\r
+// Hashtable strucAnn;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// strucAnn = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// strucAnn = new Hashtable();\r
+// }\r
+// \r
+// Vector newStruc=new Vector();\r
+// parseAnnotationRow(newStruc, type,ns);\r
+// \r
+// strucAnn.put(type, newStruc);\r
+// seqAnn.put(acc, strucAnn);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// System.err\r
+// .println("Warning - couldn't parse sequence annotation row line:\n"\r
+// + line);\r
+// // throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Unknown annotation detected: " + annType\r
+// + " " + annContent);\r
+// }\r
+// }\r
+// }\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (1 + getTreeCount());\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// }\r
+//\r
protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
String label, String annots)\r
{\r
Regex openparen = new Regex("(<|\\[)", "(");\r
Regex closeparen = new Regex("(>|\\])", ")");\r
\r
- // Detect if file is RNA by looking for bracket types\r
+ // Detect if file is RNA by looking for bracket types\r
Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
\r
convert1 = openparen.replaceAll(annots);\r
if (detectbrackets.search(pos))\r
{\r
ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getRNASecStrucState(pos).charAt(0);\r
+ .getRNASecStrucState(pos).charAt(0);\r
}\r
else\r
{\r
ann.displayCharacter = ""; // null; // " ";\r
}\r
else\r
- {\r
+ {\r
ann.displayCharacter = " " + ann.displayCharacter;\r
}\r
}\r
\r
els[i] = ann;\r
}\r
- AlignmentAnnotation annot = null;\r
+ AlignmentAnnotation annot = null;\r
Enumeration e = annotation.elements();\r
while (e.hasMoreElements())\r
{\r
annotation.addElement(annot);\r
}\r
else\r
- {\r
+ {\r
Annotation[] anns = new Annotation[annot.annotations.length\r
+ els.length];\r
- System.arraycopy(annot.annotations, 0, anns, 0,\r
- annot.annotations.length);\r
+ System.arraycopy(annot.annotations, 0, anns, 0,\r
+ annot.annotations.length);\r
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
annot.annotations = anns;\r
//System.out.println("else: ");\r
- }\r
- return annot;\r
+ }\r
+ return annot;\r
}\r
\r
public static String print(SequenceI[] s)\r
* \r
* \r
* return helicesAnnot; }\r
+ * \r
*/\r
+ /**\r
+ * make a friendly ID string.\r
+ * \r
+ * @param dataName\r
+ * @return truncated dataName to after last '/'\r
+ */\r
+ private String safeName(String dataName)\r
+ {\r
+ int b = 0;\r
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )\r
+ { \r
+ dataName = dataName.substring(b + 1).trim();\r
+ \r
+ }\r
+ int e = (dataName.length() - dataName.indexOf("."))+1;\r
+ dataName = dataName.substring(1,e).trim();\r
+ return dataName;\r
+ }\r
}\r
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
/**
* A file parse for T-Coffee score ascii format. This file contains the alignment consensus
*/
public class TCoffeeScoreFile extends AlignFile {
- public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, type);
}
- public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
});
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ alignFrameMenuBar.setBackground(Color.lightGray);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
*/
private void jbInit() throws Exception
{
+
FileMenu.setText("File");
HelpMenu.setText("Help");
VamsasMenu.setText("Vamsas");
desktopMenubar.add(VamsasMenu);
desktopMenubar.add(HelpMenu);
desktopMenubar.add(windowMenu);
+ desktopMenubar.setBackground(Color.lightGray);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
FileMenu.addSeparator();
+
package jalview.renderer;
import jalview.analysis.AAFrequency;
private int imgWidth;
- public void drawNotCanonicalAnnot(Graphics g, Annotation[] row_annotations,
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, Annotation[] row_annotations,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
+ //System.out.println(nonCanColor);
- g.setColor(NOTCANONICAL_COLOUR);
+ g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
- Regex closeparen = new Regex("(}|]|a|b|c|d)");
+ Regex closeparen = new Regex("}|]|<|a|b|c|d|e|f|g|h|i|j|k|l|m|n|o|p|q|r|s|t|u|v|w|x|y|z");
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
.equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
+ g.drawString(row_annotations[column].displayCharacter
+ , x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
+ : '-';
- if (ss == 'S')
+ if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
- ss = 's';
+
+ ss = ')';
}
}
- if (ss == 'C')
+ if (ss == '[')
{
- if ((row_annotations[column].displayCharacter.indexOf(']') > -1) || (row_annotations[column].displayCharacter.indexOf('}') > -1))
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
{
- ss = 'c';
+ ss = ']';
+
}
}
+ if (ss == '{')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ {
+ ss = '}';
+
+
+ }
+ }
+ if (ss == '<')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+
+ }
+ }
+ if (ss == 'A')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('a') > -1)
+ {
+ ss = 'a';
+
+
+ }
+ }
+
+ if (ss == 'B')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('b') > -1)
+ {
+ ss = 'b';
+
+ }
+ }
+
+ if (ss == 'C')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('c') > -1)
+ {
+ ss = 'c';
+
+ }
+ }
+ if (ss == 'D')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('d') > -1)
+ {
+ ss = 'd';
+
+ }
+ }
+ if (ss == '1')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('e') > -1)
+ {
+ ss = 'e';
+
+ }
+ }
+ if (ss == 'F')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('f') > -1)
+ {
+ ss = 'f';
+
+ }
+ }
+ if (ss == 'G')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('g') > -1)
+ {
+ ss = 'g';
+
+ }
+ }
+ if (ss == '2')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('h') > -1)
+ {
+ ss = 'h';
+
+ }
+ }
+ if (ss == 'I')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('i') > -1)
+ {
+ ss = 'i';
+
+ }
+ }
+ if (ss == 'J')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('j') > -1)
+ {
+ ss = 'j';
+
+ }
+ }
+ if (ss == 'K')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('k') > -1)
+ {
+ ss = 'k';
+
+ }
+ }
+ if (ss == 'L')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('l') > -1)
+ {
+ ss = 'l';
+
+ }
+ }
+ if (ss == 'M')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('m') > -1)
+ {
+ ss = 'm';
+
+ }
+ }
+ if (ss == 'N')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('n') > -1)
+ {
+ ss = 'n';
+
+ }
+ }
+ if (ss == 'O')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('o') > -1)
+ {
+ ss = 'o';
+
+ }
+ }
+ if (ss == 'P')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('p') > -1)
+ {
+ ss = 'p';
+
+ }
+ }
+ if (ss == 'Q')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('q') > -1)
+ {
+ ss = 'q';
+
+ }
+ }
+ if (ss == 'R')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('r') > -1)
+ {
+ ss = 'r';
+
+ }
+ }
+ if (ss == 'S')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('s') > -1)
+ {
+ ss = 's';
+
+ }
+ }
+ if (ss == 'T')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('t') > -1)
+ {
+ ss = 't';
+
+ }
+ }
+ if (ss == 'U')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('u') > -1)
+ {
+ ss = 'u';
+
+ }
+ }
+ if (ss == 'V')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('v') > -1)
+ {
+ ss = 'v';
+
+ }
+ }
+ if (ss == 'W')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('w') > -1)
+ {
+ ss = 'w';
+
+ }
+ }
+ if (ss == 'X')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('x') > -1)
+ {
+ ss = 'x';
+
+ }
+ }
+ if (ss == 'Y')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('y') > -1)
+ {
+ ss = 'y';
+
+ }
+ }
+ if (ss == 'Z')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('z') > -1)
+ {
+ ss = 'z';
+
+ }
+ }
if (!validRes || (ss != lastSS))
{
if (x > -1)
column, validRes, validEnd);
break;
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
case 'C':
case 'c':
- drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ case 'D':
+ case 'd':
+ case '1':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case '2':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ //System.out.println(lastSS);
+ Color nonCanColor= getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
default:
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
case 'c':
- case 'C':
- drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ case 'D':
+ case 'd':
+ case '1':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case '2':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ //System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
default:
private final Color STEM_COLOUR = Color.blue;
- private final Color NOTCANONICAL_COLOUR = Color.red;
+ private Color sdNOTCANONICAL_COLOUR;
public void drawGlyphLine(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
x += charWidth;
}
}
+
+
+ Color getNotCanonicalColor(char lastss)
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return Color.cyan;
+
+ case '[':
+ case ']':
+ return Color.green;
+
+ case '>':
+ case '<':
+ return Color.magenta;
+
+ case 'A':
+ case 'a':
+ return Color.orange;
+
+ case 'B':
+ case 'b':
+ return Color.pink;
+
+ case 'C':
+ case 'c':
+ return Color.red;
+
+ case 'D':
+ case 'd':
+ return Color.yellow;
+
+ case '1':
+ case 'e':
+ return Color.black;
+
+ case 'F':
+ case 'f':
+ return Color.darkGray;
+
+ case 'G':
+ case 'g':
+ return Color.gray;
+
+ case '2':
+ case 'h':
+ return Color.lightGray;
+
+ case 'I':
+ case 'i':
+ return Color.white;
+
+ case 'J':
+ case 'j':
+ return Color.cyan;
+
+ case 'K':
+ case 'k':
+ return Color.magenta;
+
+ case 'L':
+ case 'l':
+ return Color.orange;
+
+ case 'M':
+ case 'm':
+ return Color.red;
+
+ case 'N':
+ case 'n':
+ return Color.yellow;
+
+ case 'O':
+ case 'o':
+ return Color.pink;
+
+ case 'P':
+ case 'p':
+ return Color.black;
+
+ case 'Q':
+ case 'q':
+ return Color.blue;
+
+ case 'R':
+ case 'r':
+ return Color.cyan;
+
+ case 'S':
+ case 's':
+ return Color.magenta;
+
+ case 'T':
+ case 't':
+ return Color.darkGray;
+
+ case 'U':
+ case 'u':
+ return Color.yellow;
+
+ case 'V':
+ case 'v':
+ return Color.blue;
+
+ case 'W':
+ case 'w':
+ return Color.orange;
+
+ case 'X':
+ case 'x':
+ return Color.magenta;
+
+ case 'Y':
+ case 'y':
+ return Color.blue;
+
+ case 'Z':
+ case 'z':
+ return Color.blue;
+
+ default :
+ System.out.println("This is not a interaction");
+ return null;
+
+ }
+ }
}
+
+
+
public class RNAInteractionColourScheme extends ResidueColourScheme{
public RNAInteractionColourScheme()
{
- super(ResidueProperties.nucleotide, 0);
+ super();
}
/**
*/
public class ResidueColourScheme implements ColourSchemeI
{
- final int[] symbolIndex;
+ int[] symbolIndex;
boolean conservationColouring = false;
Color[] colors = null;
static
{
toRNAssState = new Hashtable();
- toRNAssState.put(")", "S");
- toRNAssState.put("(", "S");
- toRNAssState.put("]", "C");
- toRNAssState.put("[", "C");
- toRNAssState.put("{", "C");
- toRNAssState.put("}", "C");
- toRNAssState.put("A", "C");
- toRNAssState.put("a", "C");
- toRNAssState.put("B", "C");
- toRNAssState.put("b", "C");
+ toRNAssState.put(")", "(");
+ toRNAssState.put("(", "(");
+ toRNAssState.put("]", "[");
+ toRNAssState.put("[", "[");
+ toRNAssState.put("{", "{");
+ toRNAssState.put("}", "{");
+ toRNAssState.put(">", ">");
+ toRNAssState.put("<", ">");
+ toRNAssState.put("A", "A");
+ toRNAssState.put("a", "A");
+ toRNAssState.put("B", "B");
+ toRNAssState.put("b", "B");
toRNAssState.put("C", "C");
toRNAssState.put("c", "C");
- toRNAssState.put("D", "C");
- toRNAssState.put("d", "C");
+ toRNAssState.put("D", "D");
+ toRNAssState.put("d", "D");
+ toRNAssState.put("1", "1");
+ toRNAssState.put("e", "1");
+ toRNAssState.put("F", "F");
+ toRNAssState.put("f", "F");
+ toRNAssState.put("G", "G");
+ toRNAssState.put("g", "G");
+ toRNAssState.put("2", "2");
+ toRNAssState.put("h", "2");
+ toRNAssState.put("I", "I");
+ toRNAssState.put("i", "I");
+ toRNAssState.put("J", "J");
+ toRNAssState.put("j", "J");
+ toRNAssState.put("K", "K");
+ toRNAssState.put("k", "K");
+ toRNAssState.put("L", "L");
+ toRNAssState.put("l", "L");
+ toRNAssState.put("M", "M");
+ toRNAssState.put("m", "M");
+ toRNAssState.put("N", "N");
+ toRNAssState.put("n", "N");
+ toRNAssState.put("O", "O");
+ toRNAssState.put("o", "O");
+ toRNAssState.put("P", "P");
+ toRNAssState.put("p", "P");
+ toRNAssState.put("Q", "Q");
+ toRNAssState.put("q", "Q");
+ toRNAssState.put("R", "R");
+ toRNAssState.put("r", "R");
+ toRNAssState.put("S", "S");
+ toRNAssState.put("s", "S");
+ toRNAssState.put("T", "T");
+ toRNAssState.put("t", "T");
+ toRNAssState.put("U", "U");
+ toRNAssState.put("u", "U");
+ toRNAssState.put("V", "V");
+ toRNAssState.put("v", "V");
+ toRNAssState.put("W", "W");
+ toRNAssState.put("w", "W");
+ toRNAssState.put("X", "X");
+ toRNAssState.put("x", "X");
+ toRNAssState.put("Y", "Y");
+ toRNAssState.put("y", "Y");
+ toRNAssState.put("Z", "Z");
+ toRNAssState.put("z", "Z");
+
}
/**
import java.util.Hashtable;
import jalview.analysis.StructureFrequency;
+import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
try {
jalview.analysis.StructureFrequency.calculate(
- alignment.getSequencesArray(), 0, alignment.getWidth(),
- hStrucConsensus, true, rnaStruc);
+ alignment.getSequencesArray(), 0, alignment.getWidth(),
+ hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
}
}
- public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+ private String getCalcId() {
+ // TODO Auto-generated method stub
+ return null;
+}
+
+public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
{
// List<AlignmentAnnotation>
// ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public class TCoffeeScoreFileTest {
final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
@Test
- public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
@Test
- public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
try {
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
assertFalse(result.isValid());
}
@Test
- public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
assertTrue(result.isValid());
assertEquals( 8, result.getHeight() );
}
@Test
- public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
@Test
- public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());
@Test
- public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+ public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());
git://source.jalview.org / jalview.git / commitdiff