From 49207bb4d5c7b380978923817742d095b3f685b3 Mon Sep 17 00:00:00 2001 From: Charles Ofoegbu Date: Wed, 18 Mar 2015 17:05:03 +0000 Subject: [PATCH] JAL-1668 house keeping --- src/jalview/ws/dbsources/PDBRestClient.java | 23 +++---- src/jalview/ws/uimodel/PDBRestResponse.java | 99 ++++++++------------------- 2 files changed, 41 insertions(+), 81 deletions(-) diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 1a80d65..039d23f 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -148,10 +148,7 @@ public class PDBRestClient .hasNext();) { JSONObject doc = docIter.next(); - // if (doc.get("molecule_sequence") != null) - // { result.add(searchResult.new PDBResponseSummary(doc, pdbRestRequest)); - // } } searchResult.setNumberOfItemsFound(numFound); searchResult.setResponseTime(queryTime); @@ -161,13 +158,12 @@ public class PDBRestClient { e.printStackTrace(); } - return searchResult; } /** - * Takes a collection of PDBDocField and converts it into a comma delimited - * string. + * Takes a collection of PDBDocField and converts its code values into a comma + * delimited string. * * @param pdbDocfields * @return @@ -190,8 +186,9 @@ public class PDBRestClient } /** - * Determines the column index for the pdb id in the summary table. The pdb id - * serves as a unique identifier for a given row in the summary table + * Determines the column index for 'PDB Id' Fields in the dynamic summary + * table. The PDB Id serves as a unique identifier for a given row in the + * summary table * * @param wantedFeilds * the available table columns in no particular order @@ -200,16 +197,18 @@ public class PDBRestClient public static int getPDBIdColumIndex( Collection wantedFeilds, boolean hasRefSeq) { - int pdbFeildIndex = hasRefSeq ? 1 : 0; + int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; // If a reference sequence is + // attached then start counting from + // 1 else start from zero for (PDBDocField feild : wantedFeilds) { if (feild.equals(PDBDocField.PDB_ID)) { - break; + break; // once PDB Id index is determined exit iteration } - ++pdbFeildIndex; + ++pdbFeildIndexCounter; } - return pdbFeildIndex; + return pdbFeildIndexCounter; } /** diff --git a/src/jalview/ws/uimodel/PDBRestResponse.java b/src/jalview/ws/uimodel/PDBRestResponse.java index 889a324..fb227ee 100644 --- a/src/jalview/ws/uimodel/PDBRestResponse.java +++ b/src/jalview/ws/uimodel/PDBRestResponse.java @@ -26,7 +26,6 @@ import jalview.ws.dbsources.PDBRestClient.PDBDocField; import java.util.Collection; import java.util.Objects; -import javax.swing.DefaultListModel; import javax.swing.table.DefaultTableModel; import org.json.simple.JSONObject; @@ -76,24 +75,6 @@ public class PDBRestResponse this.searchSummary = searchSummary; } - /** - * Convenience method to obtain a List model for a given summary list - * - * @param summariesList - * the summary list which contains the data for generating the lists - * data - * @return the list model generated for the search summary - */ - public static DefaultListModel getListModel( - Collection summariesList) - { - DefaultListModel defaultListModel = new DefaultListModel(); - for (PDBResponseSummary summaryList : summariesList) - { - defaultListModel.addElement(summaryList); - } - return defaultListModel; - } /** * Convenience method to obtain a Table model for a given summary List and @@ -110,22 +91,25 @@ public class PDBRestResponse public static DefaultTableModel getTableModel(PDBRestRequest request, Collection summariesList) { - DefaultTableModel model = new DefaultTableModel(); + DefaultTableModel tableModel = new DefaultTableModel(); if (request.getAssociatedSequence() != null) { - model.addColumn("Sequence"); + tableModel.addColumn("Sequence"); // Create sequence column header if + // exists in the request } for (PDBDocField field : request.getWantedFields()) { - model.addColumn(field.getName()); + tableModel.addColumn(field.getName()); // Create sequence column header if + // exists in the request } for (PDBResponseSummary res : summariesList) { - model.addRow(res.getSummaryData()); + tableModel.addRow(res.getSummaryData()); // Populate table rows with + // summary list } - return model; + return tableModel; } /** @@ -138,49 +122,40 @@ public class PDBRestResponse { private String pdbId; - private String concatenatedSummaryData; - - private String[] summaryData; + private String[] summaryRowData; private String associatedSequence; - private int width = 480; - public PDBResponseSummary(JSONObject doc, PDBRestRequest request) { - StringBuilder summaryBuilder = new StringBuilder(); Collection diplayFields = request.getWantedFields(); String associatedSeq = request.getAssociatedSequence(); int colCounter = 0; - summaryData = new String[(associatedSeq != null) ? diplayFields + summaryRowData = new String[(associatedSeq != null) ? diplayFields .size() + 1 : diplayFields.size()]; if (associatedSeq != null) { this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq .substring(0, 18) : associatedSeq; - summaryData[0] = associatedSequence; + summaryRowData[0] = associatedSequence; colCounter = 1; } for (PDBDocField field : diplayFields) { + String fieldData = (doc.get(field.getCode()) == null) ? "" : doc + .get(field.getCode()).toString(); if (field.equals(PDBDocField.PDB_ID) && doc.get(PDBDocField.PDB_ID.getCode()) != null) { - this.pdbId = doc.get(PDBDocField.PDB_ID.getCode()).toString(); - summaryData[colCounter++] = this.pdbId; + this.pdbId = fieldData; + summaryRowData[colCounter++] = this.pdbId; } else { - String value = (doc.get(field.getCode()) == null) ? "" : doc.get( - field.getCode()).toString(); - summaryBuilder.append(field.getName()).append(": ").append(value) - .append(" | "); - summaryData[colCounter++] = value; + summaryRowData[colCounter++] = fieldData; } } - this.concatenatedSummaryData = summaryBuilder.toString(); - summaryBuilder = null; } public String getPdbId() @@ -193,56 +168,42 @@ public class PDBRestResponse this.pdbId = pdbId; } - public String getConcatenatedSummaryData() - { - return concatenatedSummaryData; - } - - public void setConcatenatedSummaryData(String concatenatedSummaryData) - { - this.concatenatedSummaryData = concatenatedSummaryData; - } - public String[] getSummaryData() { - return summaryData; + return summaryRowData; } public void setSummaryData(String[] summaryData) { - this.summaryData = summaryData; + this.summaryRowData = summaryData; } + @Override public String toString() { - StringBuilder html = new StringBuilder(); - html.append("
"); - html.append(concatenatedSummaryData); - html.append("
"); - return html.toString(); + StringBuilder summaryFieldValues = new StringBuilder(); + for (String summaryField : summaryRowData) + { + summaryFieldValues.append(summaryField).append("\t"); + } + return summaryFieldValues.toString(); } @Override public int hashCode() { - return Objects.hash(this.pdbId, this.concatenatedSummaryData); + return Objects.hash(this.pdbId, this.toString()); } @Override - public boolean equals(Object other) + public boolean equals(Object that) { - if (!(other instanceof PDBResponseSummary)) + if (!(that instanceof PDBResponseSummary)) { return false; } - - PDBResponseSummary that = (PDBResponseSummary) other; - - // Custom equality check here. - return this.pdbId.equals(that.pdbId) - && this.concatenatedSummaryData - .equals(that.concatenatedSummaryData); + PDBResponseSummary another = (PDBResponseSummary) that; + return this.toString().equals(another.toString()); } } -- 1.7.10.2