From 9653b3fbb4f959cba2aa93916b96a576afc98848 Mon Sep 17 00:00:00 2001
From: Ryan Wick <rrwick@gmail.com>
Date: Wed, 15 Jul 2015 13:15:25 +1000
Subject: [PATCH] Add error if query option used in wrong place

---
 command_line/commoncommandlinefunctions.cpp | 3 +++
 program/globals.h                           | 2 ++
 program/main.cpp                            | 2 ++
 program/settings.cpp                        | 2 ++
 program/settings.h                          | 2 ++
 5 files changed, 11 insertions(+)

diff --git a/command_line/commoncommandlinefunctions.cpp b/command_line/commoncommandlinefunctions.cpp
index fae93afb..8f5f99a6 100644
--- a/command_line/commoncommandlinefunctions.cpp
+++ b/command_line/commoncommandlinefunctions.cpp
@@ -166,6 +166,9 @@ QString checkForInvalidOrExcessSettings(QStringList * arguments)
     error = checkOptionForInt("--distance", arguments, 0, 100);
     if (error.length() > 0) return error;
 
+    if (isOptionPresent("--query", arguments) && g_settings->commandLineCommand == NO_COMMAND)
+        return "The --query option can only be used with Bandage load and Bandage image";
+
     error = checkOptionForFile("--query", arguments);
     if (error.length() > 0) return error;
     error = checkOptionForString("--blastp", arguments, QStringList(), "blastn/tblastn parameters");
diff --git a/program/globals.h b/program/globals.h
index 42341884..21b1ba3a 100644
--- a/program/globals.h
+++ b/program/globals.h
@@ -40,6 +40,8 @@ enum GraphFileType {LAST_GRAPH, FASTG, GFA, TRINITY, ANY_FILE_TYPE, UNKNOWN_FILE
 enum SequenceType {NUCLEOTIDE, PROTEIN, EITHER_NUCLEOTIDE_OR_PROTEIN};
 enum BlastUiState {BLAST_DB_NOT_YET_BUILT, BLAST_DB_BUILD_IN_PROGRESS, BLAST_DB_BUILT_BUT_NO_QUERIES,
                    READY_FOR_BLAST_SEARCH, BLAST_SEARCH_IN_PROGRESS, BLAST_SEARCH_COMPLETE};
+enum CommandLineCommand {NO_COMMAND, BANDAGE_LOAD, BANDAGE_IMAGE};
+
 
 extern QSharedPointer<Settings> g_settings;
 extern MyGraphicsView * g_graphicsView;
diff --git a/program/main.cpp b/program/main.cpp
index d846bdde..f100fba6 100644
--- a/program/main.cpp
+++ b/program/main.cpp
@@ -81,11 +81,13 @@ int main(int argc, char *argv[])
         if (first == "load")
         {
             arguments.pop_front();
+            g_settings->commandLineCommand = BANDAGE_LOAD;
             return bandageLoad(&a, arguments);
         }
         else if (first == "image")
         {
             arguments.pop_front();
+            g_settings->commandLineCommand = BANDAGE_IMAGE;
             return bandageImage(arguments);
         }
 //        else if (first == "contiguous")
diff --git a/program/settings.cpp b/program/settings.cpp
index 4c8ee04d..cd3e5bbe 100644
--- a/program/settings.cpp
+++ b/program/settings.cpp
@@ -103,6 +103,8 @@ Settings::Settings()
     blastSearchParameters = "";
 
     rememberedPath = QDir::homePath();
+
+    commandLineCommand = NO_COMMAND;
 }
 
 
diff --git a/program/settings.h b/program/settings.h
index d518db7d..e80e7386 100644
--- a/program/settings.h
+++ b/program/settings.h
@@ -113,6 +113,8 @@ class Settings
 
     QString rememberedPath;
 
+    CommandLineCommand commandLineCommand;
+
     bool anyNodeDisplayText() {return displayNodeCustomLabels || displayNodeNames || displayNodeLengths || displayNodeCoverages;}
     int getBasePairsPerSegment();
 };