start MITAB

MI-JSON.js

@@ -1,40 +1,40 @@
 /* JSON format for PSI-MI data.
  * - first attempt, change it if you think terminology or structure is wrong.
- * 
+ *
  * *Overview*
  * An array of Interactors, each with:
  *      sequence,
  *      type (values are "protein", "bioactive entity", "gene", or "nucliec acid"),
  *      organism,
  *      accession,
  *      label,
- *      array of features (such as PTM's), each with:
+ *      array of features (such as PTM's, i.e. unlinked features), each with:
  *          name,
  *          start residue (1 based),
  *          end residue (1 based)
  *      meta? - you could put any other relevant info in here?
  *      [TODO: add information about membership of complexes (parent node)
- *       and stochiometry in order to make complex viewer :) ] 
+ *       and stochiometry in order to make complex viewer :) ]
  *
  *then an array of Interactions, each with:
  *      source accession,
  *      target accession,
  *      an array of linked features
- * 
+ *
  *      for each linked feature:
  *          evidence,
  *          source binding sites (string, see below),
  *          target binding sites (string, see below),
  *          meta? - you could put any other relevant info in here? publication?
- *      
+ *
  * Strings describing binding sites (MI-TAB like)
  *      - comma seperated list of binding sites,
- *          - binding sites can be specific residue, range with or without fuzzy 
- *            boundaries, fuzzy range, greater than, less than, 
- *            or keywords for unknown, n/c terminus, n/c terminus range   
- *      
+ *          - binding sites can be specific residue, range with or without fuzzy
+ *            boundaries, fuzzy range, greater than, less than,
+ *            or keywords for unknown, n/c terminus, n/c terminus range
+ *
  *      - i.e. a comma seperated list of any of the following (numerical values are 1 based):
- *              
+ *
  *              "?" = unknown (represented as link to circle beside interactors label)
  *              "n" = residue 1
  *              "c" = residue at interactor.sequence.length
@@ -45,32 +45,31 @@
  *              "86..123-456..464" = residue range with fuzzy boundaries
  *              "86..123-456" = residue range with one fuzzy boundary
  *              "23..45" = fuzzy range
- *              "<8" = range between 0 and 8
+ *              "<8" = range between 1 and 8
  *              ">256" = range between 256 and interactor.sequence.length
- *              
  */
 
 
 //example
 var miData = {
     "interactors": [
         {
-            "sequence": "AREALLYLONGLISTOFCAPITALLETTERS",
+            "sequence": "MAATAAAVVAEEDTELRDLLVQTLENSGVLNRIKAELRAAVFLALEEQEKVENKTPLVNESLKKFLNTKDGRLVASLVAEFLQFFNLDFTLAVFQPETSTLQGLEGRENLARDLGIIEAEGTVGGPLLLEVIRRCQQKEKGPTTGEGALDLSDVHSPPKSPEGKTSAQTTPSKIPRYKGQGKKKTSGQKAGDKKANDEANQSDTSVSLSEPKSKSSLHLLSHETKIGSFLSNRTLDGKDKAGLCPDEDDMEGDSFFDDPIPKPEKTYGLRKEPRKQAGSLASLSDAPPLKSGLSSLAGAPSLKDSESKRGNTVLKDLKLISDKIGSLGLGTGEDDDYVDDFNSTSHRSEKSEISIGEEIEEDLSVEIDDINTSDKLDDLTQDLTVSQLSDVADYLEDVA",
             "type": "protein",
             "organism": "penguin",
             "accession": "P1",
             "label": "Quentin",
             "meta": {"fruit": "apple"}
         },
         {
-            "sequence": "ANOTHERAREALLYLONGLISTOFCAPITALLETTERS",
+            "sequence": "MCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSGMCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG",
             "type": "protein",
             "organism": "penguin",
             "accession": "P2",
             "label": "Justin"
         },
         {
-            "sequence": "ANOTHERAREALLYLONGLISTOFCAPITALLETTERSAGAIN",
+            "sequence": "ANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAINANOTHERREALLYLONGLISTOFCAPITALLETTERSAGAIN",
             "type": "protein",
             "organism": "penguin",
             "accession": "P3",
@@ -80,13 +79,13 @@ var miData = {
     ],
     "interactions": [
         {
-            "target": "P1",
             "source": "P2",
+            "target": "P1",
             "linkedFeatures": [
                 {
                     "evidence": "mass spec/cross-linking",
                     "sourceSites": "128",
-                    "targetSites": "987"
+                    "targetSites": "350"
                 },
                 {
                     "evidence": "Y2H",
@@ -96,8 +95,8 @@ var miData = {
             ]
         },
         {
-            "target": "P3",
             "source": "P2",
+            "target": "P3",
             "linkedFeatures": [
                 {
                     "evidence": "tarot cards",

NOTICE

@@ -1,6 +1,5 @@
-      xiNET interaction viewer
-      Copyright 2013 Rappsilber Laboratory
-
-      This product includes software developed at
-      the Rappsilber Laboratory (http://www.rappsilberlab.org/).
-
+//    xiNET interaction viewer
+//    Copyright 2013 Rappsilber Laboratory
+//
+//    This product includes software developed at
+//    the Rappsilber Laboratory (http://www.rappsilberlab.org/).

demo.css

@@ -8,7 +8,7 @@ html, body, #outerDiv  {
 }
 
 p{
-    margin-left:8px;
+    margin:8px;
 }
 #leftColumn{
     width: 228px;
@@ -44,7 +44,7 @@ fieldset{
     padding: 8px;
 }
 input, select, button {
-    max-width: 171px;
+    /*max-width: 171px;*/
     margin:2px;
     margin-top:4px;
 }