Merge pull request #16 from gamcil/master

Use Foldseek-specific result HTML
steineggerlab · May 20, 2022 · 2dd3b2f · 2dd3b2f
2 parents d3c0a6a + 01ef395
commit 2dd3b2f
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Showing 4 changed files with 17 additions and 6 deletions.
diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
@@ -9,6 +9,7 @@ set(COMPILED_RESOURCES
         mat3di.out
         encoder_weights_3di.kerasify
         evalue_nn.kerasify
+	result_viz_prelude_fs.html.zst
         )
 
 set(GENERATED_OUTPUT_HEADERS "")

diff --git a/data/result_viz_prelude_fs.html.zst b/data/result_viz_prelude_fs.html.zst
diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -118,6 +118,7 @@ std::vector<int> LocalParameters::getOutputFormat(int formatMode, const std::str
     if (formatMode == Parameters::FORMAT_ALIGNMENT_SAM || formatMode == Parameters::FORMAT_ALIGNMENT_HTML) {
         needSequences = true;
         needBacktrace = true;
+	needCa = true;
         return formatCodes;
     }
     std::vector<std::string> outformatSplit = Util::split(outformat, ",");

diff --git a/src/strucclustutils/structureconvertalis.cpp b/src/strucclustutils/structureconvertalis.cpp
@@ -17,9 +17,7 @@
 
 
 #include <zstd.h>
-namespace viz{
-#include "result_viz_prelude.html.zst.h"
-}
+#include "result_viz_prelude_fs.html.zst.h"
 #include <map>
 
 #ifdef OPENMP
@@ -344,9 +342,9 @@ int structureconvertalis(int argc, const char **argv, const Command &command) {
         }
         delete[] headerWritten;
     } else if (format == Parameters::FORMAT_ALIGNMENT_HTML) {
-        size_t dstSize = ZSTD_findDecompressedSize(viz::result_viz_prelude_html_zst, viz::result_viz_prelude_html_zst_len);
+        size_t dstSize = ZSTD_findDecompressedSize(result_viz_prelude_fs_html_zst, result_viz_prelude_fs_html_zst_len);
         char* dst = (char*)malloc(sizeof(char) * dstSize);
-        size_t realSize = ZSTD_decompress(dst, dstSize, viz::result_viz_prelude_html_zst, viz::result_viz_prelude_html_zst_len);
+        size_t realSize = ZSTD_decompress(dst, dstSize, result_viz_prelude_fs_html_zst, result_viz_prelude_fs_html_zst_len);
         resultWriter.writeData(dst, realSize, 0, 0, false, false);
         const char* scriptBlock = "<script>render([";
         resultWriter.writeData(scriptBlock, strlen(scriptBlock), 0, 0, false, false);
@@ -441,6 +439,10 @@ int structureconvertalis(int argc, const char **argv, const Command &command) {
                 } else {
                     result.append(querySeqData, querySeqLen);
                 }
+                result.append("\", \"qca\": \"");
+                caStr.clear();
+                caToStr(queryCaData, querySeqLen, caStr);
+                result.append(caStr, 0, caStr.size()-1);
                 result.append("\"}, \"alignments\": [\n");
             }
 
@@ -769,7 +771,6 @@ int structureconvertalis(int argc, const char **argv, const Command &command) {
                                              res.dbStartPos + 1, res.dbEndPos + 1,
                                              res.eval, res.score,
                                              res.qLen, res.dbLen);
-
                         if (count < 0 || static_cast<size_t>(count) >= sizeof(buffer)) {
                             Debug(Debug::WARNING) << "Truncated line in entry" << i << "!\n";
                             continue;
@@ -799,6 +800,14 @@ int structureconvertalis(int argc, const char **argv, const Command &command) {
                                                (res.dbStartPos > res.dbEndPos),
                                                (isTranslatedSearch == true && targetNucs == true), translateNucl);
                         }
+                        result.append("\", \"tca\": \"");
+                        caStr.clear();
+                        caToStr(targetCaData, res.dbLen, caStr);
+                        result.append(caStr, 0, caStr.size()-1);
+
+                        result.append("\", \"tseq\": \"");
+                        result.append(targetSeqData, 0, res.dbLen);
+
                         result.append("\" },\n");
                         break;
                     }