From: tcofoegbu Date: Mon, 27 Apr 2015 14:24:09 +0000 (+0100) Subject: JAL-1714 improved the new PDB Sequence fetcher by enabling it query multiple PDB... X-Git-Tag: Jalview_2_9~46^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c9764f63ef34188eee34d2a6958efdc3d2f74e71;p=jalview.git JAL-1714 improved the new PDB Sequence fetcher by enabling it query multiple PDB entries in one operation --- diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java index 5a8407a..514406a 100644 --- a/src/jalview/gui/PDBSearchPanel.java +++ b/src/jalview/gui/PDBSearchPanel.java @@ -74,19 +74,16 @@ public class PDBSearchPanel extends GPDBSearchPanel wantedFields = PDBDocFieldPreferences .getSearchSummaryFields(); - String searchTerm = txt_search.getText(); - if (searchTerm.contains(":")) - { - searchTerm = searchTerm.split(":")[0]; - } + String searchTerm = decodeSearchTerm(txt_search.getText(), + searchTarget); PDBRestRequest request = new PDBRestRequest(); request.setAllowEmptySeq(allowEmptySequence); request.setResponseSize(100); - request.setFieldToSearchBy(searchTarget + ":"); - request.setSearchTerm(searchTerm); + request.setFieldToSearchBy("(" + searchTarget + ":"); + request.setSearchTerm(searchTerm + ")"); request.setWantedFields(wantedFields); - + // System.out.println(">>>>>>>>>>>>>> " + request.getQuery()); PDBRestClient pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList = pdbRestCleint.executeRequest(request); if (resultList.getSearchSummary() != null) @@ -105,6 +102,43 @@ public class PDBSearchPanel extends GPDBSearchPanel } } + public static String decodeSearchTerm(String enteredText, + String targetField) + { + String foundSearchTerms = enteredText; + StringBuilder foundSearchTermsBuilder = new StringBuilder(); + if (enteredText.contains(";")) + { + String[] searchTerms = enteredText.split(";"); + for (String searchTerm : searchTerms) + { + if (searchTerm.contains(":")) + { + foundSearchTermsBuilder.append(targetField).append(":") + .append(searchTerm.split(":")[0]).append(" OR "); + } + else + { + foundSearchTermsBuilder.append(targetField).append(":") + .append(searchTerm).append(" OR "); + } + } + int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR "); + foundSearchTerms = foundSearchTermsBuilder.toString(); + if (foundSearchTerms.contains(" OR ")) + { + foundSearchTerms = foundSearchTerms.substring( + targetField.length() + 1, endIndex); + } + } + else if (enteredText.contains(":")) + { + foundSearchTerms = foundSearchTerms.split(":")[0]; + } + return foundSearchTerms; + } + + @Override public void btn_ok_ActionPerformed() { @@ -139,23 +173,43 @@ public class PDBSearchPanel extends GPDBSearchPanel .toString(); String searchTerm = txt_search.getText(); - if (searchTerm.contains(":")) - { - selectedIds.append(";").append(pdbIdStr).append(":") - .append(searchTerm.split(":")[1].toUpperCase()); - } - else - { - selectedIds.append(";").append(pdbIdStr); - } + selectedIds.append(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm)) + .append(";"); } - String ids = selectedIds.deleteCharAt(0).toString(); + String ids = selectedIds.toString(); + // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids); seqFetcher.textArea.setText(ids); Thread worker = new Thread(seqFetcher); worker.start(); } + public static String getPDBIdwithSpecifiedChain(String pdbId, + String searchTerm) + { + String pdbIdWithChainCode = ""; + if (searchTerm.contains(";")) + { + String[] foundTerms = searchTerm.split(";"); + for (String foundTerm : foundTerms) + { + if (foundTerm.contains(pdbId)) + { + pdbIdWithChainCode = foundTerm; + } + } + } + else if (searchTerm.contains(pdbId)) + { + pdbIdWithChainCode = searchTerm; + } + else + { + pdbIdWithChainCode = pdbId; + } + return pdbIdWithChainCode; + } + /** * Populates search target combo-box options */ diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index c913213..cd4faf6 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -237,7 +237,7 @@ public class StructureChooser extends GStructureChooser String[] names = seqName.toLowerCase().split("\\|"); for (String name : names) { - System.out.println("Found name : " + name); + // System.out.println("Found name : " + name); name.trim(); if (isValidSeqName(name)) { diff --git a/test/jalview/gui/PDBSearchPanelTest.java b/test/jalview/gui/PDBSearchPanelTest.java index 17ba85a..4595ad1 100644 --- a/test/jalview/gui/PDBSearchPanelTest.java +++ b/test/jalview/gui/PDBSearchPanelTest.java @@ -1,5 +1,6 @@ package jalview.gui; +import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; import javax.swing.JInternalFrame; @@ -31,6 +32,43 @@ public class PDBSearchPanelTest } @Test + public void testDecodeSearchTerm() + { + String expectedString = "1xyz OR text:2xyz OR text:3xyz"; + String outcome = PDBSearchPanel.decodeSearchTerm("1xyz:A;2xyz;3xyz", + "text"); + // System.out.println("1 >>>>>>>>>>> " + outcome); + assertEquals(expectedString, outcome); + + expectedString = "1xyz"; + outcome = PDBSearchPanel.decodeSearchTerm("1xyz", "text"); + // System.out.println("2 >>>>>>>>>>> " + outcome); + assertEquals(expectedString, outcome); + } + + @Test + public void testgetPDBIdwithSpecifiedChain() + { + + String expectedString = "1xyz:A"; + String outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("1xyz", + "2xyz;3xyz;1xyz:A"); + System.out.println("1 >>>>>>>>>>> " + outcome); + assertEquals(expectedString, outcome); + + expectedString = "2xyz"; + outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("2xyz", + "1xyz:A;2xyz;3xyz"); + System.out.println("2 >>>>>>>>>>> " + outcome); + assertEquals(expectedString, outcome); + + expectedString = "2xyz:A"; + outcome = PDBSearchPanel.getPDBIdwithSpecifiedChain("2xyz", "2xyz:A"); + System.out.println("3 >>>>>>>>>>> " + outcome); + assertEquals(expectedString, outcome); + } + + @Test public void txt_search_ActionPerformedTest() { PDBSearchPanel searchPanel = new PDBSearchPanel(null); @@ -47,4 +85,5 @@ public class PDBSearchPanelTest assertTrue(!mainFrame.getTitle().equalsIgnoreCase( "PDB Sequence Fetcher")); } + }