From 171ca8730ea146d50b2eb00701d8df986d88f519 Mon Sep 17 00:00:00 2001 From: Anne Menard Date: Mon, 16 Jul 2012 11:17:19 +0200 Subject: [PATCH] Last version --- src/MCview/PDBfile.java | 21 +- .../schemes/RNAInteractionColourScheme.java | 65 ++++++ src/jalview/ws/jws1/Annotate3D.java | 206 ++++++++++++++++++++ 3 files changed, 282 insertions(+), 10 deletions(-) create mode 100644 src/jalview/schemes/RNAInteractionColourScheme.java create mode 100644 src/jalview/ws/jws1/Annotate3D.java diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index dede37e..048f639 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -182,24 +182,25 @@ public class PDBfile extends jalview.io.AlignFile seqs.addElement(chainseq); if(isRNA(chainseq)==true) { + String path =inFile.getPath(); System.out.println("this is a PDB format and RNA sequence"); - Annotate3D an3d = new Annotate3D(id); + Annotate3D an3d = new Annotate3D(path); System.out.println(id); //BufferedWriter r = an3d.getReader(); - BufferedReader in = new BufferedReader(new FileReader("temp.rnaml")); + // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml")); - String str; - while ((str = in.readLine()) != null) { - System.out.println(str); - System.out.println("toto"); + //String str; + // while ((str = in.readLine()) != null) { + // System.out.println(str); + // System.out.println("toto"); - } - String type = "File"; - RnamlFile rnaml =new RnamlFile("temp.rnaml",type); + // } + //String type = "File"; + //RnamlFile rnaml =new RnamlFile("temp.rnaml",type); System.out.println("Create rnamfile object"); //rnaml.parse("temp"); - this.annotations =rnaml.getAnnot(); + //this.annotations =rnaml.getAnnot(); } diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java new file mode 100644 index 0000000..3197caf --- /dev/null +++ b/src/jalview/schemes/RNAInteractionColourScheme.java @@ -0,0 +1,65 @@ +package jalview.schemes; + +import jalview.datamodel.SequenceI; + +import java.awt.Color; + + +public class RNAInteractionColourScheme extends ResidueColourScheme{ + public RNAInteractionColourScheme() + { + super(ResidueProperties.nucleotide, 0); + } + + /** + * DOCUMENT ME! + * + * @param n + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public Color findColour(char c) + { + // System.out.println("called"); log.debug + return colors[ResidueProperties.nucleotideIndex[c]]; + } + + /** + * DOCUMENT ME! + * + * @param n + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public Color findColour(char c, int j, SequenceI seq) + { + Color currentColour; + if ((threshold == 0) || aboveThreshold(c, j)) + { + try + { + currentColour = colors[ResidueProperties.nucleotideIndex[c]]; + } catch (Exception ex) + { + return Color.white; + } + } + else + { + return Color.white; + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + + return currentColour; + } + } diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java new file mode 100644 index 0000000..505e15f --- /dev/null +++ b/src/jalview/ws/jws1/Annotate3D.java @@ -0,0 +1,206 @@ +package jalview.ws.jws1; + +import java.io.BufferedInputStream; +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.DataInputStream; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.FileWriter; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStream; +import java.io.OutputStreamWriter; +import java.io.Reader; +import java.io.StringWriter; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; +import java.net.URLConnection; + +import java.net.URLEncoder; + + + +public class Annotate3D { + //protected BufferedReader in; + //protected BufferedWriter out; + + public Annotate3D() + { + System.out.println("Annotate3D"); + //try { + // Create a URL for the desired page + //String id = "1HR2"; + //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id); + //in = new BufferedReader(new InputStreamReader(url.openStream())); + //String str; + //OutputStream out1 = null; + //out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml")); + //while ((str = in.readLine()) != null) { + //System.out.println(str); + //out.write(str); + //} + //in.close(); + //out.close(); + //} catch (MalformedURLException e) { + //} catch (IOException e) { + //} + } + + public Annotate3D(String path) throws InterruptedException{ + System.out.println("Annotate3D"); + try { +// //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile); +// System.out.println("Step1"); +// FileReader r = new FileReader(inFile); +// BufferedReader in = new BufferedReader(r); +// StringBuffer content = new StringBuffer(); +// System.out.println("Step2"); +// while(in.readLine()!=null){ +// content.append(in.readLine()); +// //System.out.println("Step3"+in.readLine()); +// } +// +// String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8"); +// for (int i=0;i